Method for detecting at least one mechanism of resistance to glycopeptides by mass spectrometry

ABSTRACT

A method of detection, for at least one microorganism contained in a sample, of at least one marker of resistance to a glycopeptide, including the detection, by mass spectrometry, of at least one peptide or protein of the microorganism. Preferably, the glycopeptide is vancomycin. Preferably, the peptide is derived from a protein of type vanA, vanB, vanC, vanD, vanE, vanG, vanL, vanM or vanN.

The present invention relates to the field of microbiology. More precisely, the invention relates to the detection, by mass spectrometry, of at least one mechanism of resistance to glycopeptides of at least one microorganism obtained from a sample.

Since the discovery of microbes by Pasteur, microorganisms have been studied by microscopy and biochemical analyses. These traditional methods are often long and tedious and analytical alternatives were soon required. Thus, analysis of bacteria by mass spectrometry was begun in 1975 by J. Anhalt and C. Fenselau [1].

This preliminary work was followed by the use of gas chromatography coupled to mass spectrometry (GC-MS) for studying fatty acids of the cell wall of microorganisms [2]. This method became popular under the English name FAME for Fatty Acid Methyl Ester. It now constitutes a reference method for taxonomic studies. However, its use is still limited to certain specialized laboratories able to treat the sample by saponification, hydrolysis and derivation.

In 1996, the works of M. Claydon et al. [3] and of T. Krishnamurthy and P. Ross [4] showed that it is possible to identify various bacterial species with a mass spectrometer of the MALDI-TOF type (Matrix Assisted Laser Desorption Ionization-Time Of Flight). Analysis combines acquisition of a mass spectrum and interpretation by expert software. It is extremely simple and can be performed in a few minutes. It is currently being adopted in medical analysis laboratories [5]. Its clinical use, however, is limited to identification of bacterial species and yeasts. It is not used routinely for identifying resistance to antimicrobials.

Now, identification of resistance to antimicrobials such as antibiotics is an essential element for ensuring optimal patient management.

Other methods of mass spectrometry, notably in tandem, have been proposed for addressing these needs. As an example, we may mention the works of C. Fenselau et al., for identifying β-lactamase with a quadrupole-TOF (Q-TOF) [6]. However, these research results are not applicable to routine clinical use. They were obtained with research instruments requiring highly qualified personnel. The analysis times, often more than one hour per sample, are incompatible with the workload of a microbiological analysis laboratory.

More recently, S. Hofstadler et al. [7] proposed a method combining amplification of the microbial genome by PCR with detection of the PCR products by electrospray-TOF (ESI-TOF). This method is now fully automated [8]. However, it requires amplification by PCR with the inherent faults of molecular biology, namely extraction yield, cost of probes, etc.

In this context, the aim of the present invention is to propose a method for detecting mechanisms of resistance to glycopeptides that allows the drawbacks of the methods of the prior art to be overcome, namely to supply a low-cost method, without a reagent specific to each species, notably relative to the methods of molecular biology, giving a result in a short time, less than one hour, and usable in routine clinical practice, without requiring highly qualified personnel.

For this purpose, the invention proposes a new method of detection, for at least one microorganism contained in a sample, of at least one marker of resistance to a glycopeptide, comprising the detection, by mass spectrometry, of at least one peptide or protein of said microorganism.

Advantageously, markers of resistance to several different antimicrobials can be detected simultaneously.

Surprisingly and unexpectedly, the method of the present invention makes it possible to detect the existence of inducible mechanisms of resistance, in the absence of induction.

As indicated in application WO2011045544, markers of typing and/or of virulence of microorganisms can be detected, in the same way, by mass spectrometry, prior to or simultaneously with detection of the mechanism of resistance markers.

“Markers of resistance to at least one antimicrobial of the class of glycopeptides” means molecules of protein origin that are characteristic of said properties of resistance.

The glycopeptides are antibiotics such as vancomycin, teicoplanin, telavancin, bleomycin, ramoplanin, and decaplanin. Vancomycin is a glycopeptide proper, teicoplanin is a lipoglycopeptide. These two molecules inhibit synthesis of the bacterial wall by inhibition of the synthesis of the peptidoglycan. In fact, their pocket-shaped three-dimensional structure covers the dipeptide D-Ala D-Ala precursor of synthesis of the peptidoglycan, prevents the action of glycosyltransferases and transpeptidases and blocks elongation of the peptidoglycan. Resistance to glycopeptides is due to the presence of operons encoding enzymes catalyzing the formation of low-affinity precursors and enzymes eliminating the high-affinity precursors produced by the host bacterium. Various types of resistance are known, depending on the enzymes present in the operon. Classification of resistance to glycopeptides is based on the primary sequence of the structural genes of the resistance ligases rather than on the levels of resistance to the glycopeptides, to the extent that the minimum inhibitory concentrations (MIC) of the various types overlap. Nine types of resistance have been identified. Eight result from acquired resistance (VanA, B, D, E, G, L, M and N) and one (VanC) is a natural resistance present in E. gallinarum and to E. casseliflavus. (for a review see [9], Sujatha, S. & Praharaj, I. Glycopeptide Resistance in Gram-Positive Cocci: A Review. Interdiscip. Perspect. Infect. Dis 2012, 781679 (2012))

The VanA type of resistance is characterized by a high-level inducible resistance to vancomycin and to teicoplanin. Note that transmission of the VanA type to S. aureus has been demonstrated but is nevertheless quite rare.

The VanB type of resistance is characterized by an inducible resistance of moderate to high level to vancomycin and is sensitive to teicoplanin.

In general, the VanA and VanB phenotypes are the most important clinical cases and are frequently found in E. faecalis and in E. faecium.

The VanD type of resistance is characterized by a constitutive resistance of moderate level to vancomycin and to teicoplanin.

The types of resistance VanC, E, G, L and N are characterized by a low-level resistance to vancomycin and by sensitivity to teicoplanin.

Resistance may be expressed in the absence of antibiotic, it is then called constitutive. It may also be expressed in the presence of a certain concentration of antibiotic, it is then called inducible. Culture of the microorganism in the presence of a certain concentration of antibiotic is then called culture with induction.

Determination of resistance to at least one antimicrobial means that it is impossible to destroy the bacteria or inhibit their multiplication at a defined concentration as a function of the pharmacodynamic and pharmacokinetic parameters characteristic of each antibiotic.

Determination of a mechanism of resistance to at least one antibiotic means detecting at least one compound synthesized by the bacterium, enabling it to evade, at least partially, the action of the antibiotic, most often by modification of the structure of the antibiotic or of its metabolic target, or else by its reduced penetration into the bacterium. Preferably, said compound synthesized by the bacterium is a protein.

The method of the invention may be employed for detecting mechanisms of resistance to glycopeptides in bacteria. Thus, for example, as bacteria for which it is possible to investigate a mechanism of resistance to glycopeptides according to the method of the invention, we may mention, nonexhaustively: Enterococcus faecalis, Enterococcus faecium, Enterococcus gallinarum, Enterococcus casseliflavus, Enterococcus durans, Enterococcus avium, Enterococcus raffinosus or Staphylococcus aureus. The agents primarily responsible for infections are the Enterococci and more particularly Enterococcus faecalis and Enterococcus faecium.

Thus, the method according to the invention also makes it possible to detect a mechanism of resistance to said antibiotics.

“Sample” means a small part or small isolated amount of an entity for analysis. The sample on which the method of the invention may be implemented is any sample that may contain a target microorganism. The sample may be of biological origin, either animal, vegetable or human. It may then correspond to a sample of biological fluid (whole blood, serum, plasma, urine, cerebrospinal fluid, organic secretion, for example), a tissue sample or isolated cells. This sample may be used as it is, i.e. the markers of the mechanisms of resistance of the bacteria to glycopeptides are potentially detectable directly in the sample tested, or else it may undergo, prior to analysis, a preparation such as enrichment, extraction, concentration, purification, culture, according to methods known by a person skilled in the art.

The sample may be of industrial origin, or, according to a nonexhaustive list, a sample of air, a sample of water, a sample taken from a surface, an article or a manufactured product, a product of food origin. Among the samples of food origin, we may mention nonexhaustively a sample of a milk product (yoghurts, cheeses), of meat, of fish, of egg, of fruit, of vegetable, of water, of drink (milk, fruit juice, soda, etc.). These samples of food origin may also come from sauces or from prepared dishes. A food sample may finally be obtained from feed intended for animals, notably such as animal feed meal.

Upstream of detection by mass spectrometry, the sample to be analyzed is preferably treated beforehand to generate peptides from all of the proteins present in the sample, to fragment these proteins into peptides, for example by digestion with a proteolytic enzyme (protease), or by the action of a chemical reagent. In fact, cleavage of the proteins may be brought about by a physicochemical treatment, by a biological treatment or by a combination of both treatments. Among the treatments usable, we may mention treatment with hydroxyl radicals, notably with H₂O₂. Treatment with hydroxyl radicals causes cleavage of the peptide bonds, which occurs randomly on any peptide bond of the protein. The concentration of hydroxyl radicals determines the number of cleavages performed and therefore the length of the peptide fragments obtained. Other chemical treatments may also be used, such as, for example, treatment with cyanogen bromide (BrCN) which specifically cleaves the peptide bonds at the level of the carboxyl group of the methionyl residues. It is also possible to perform partial acid cleavage at the level of the aspartyl residues by heating a solution of proteins in trifluoroacetic acid at 1000° C.

Treatment of the proteins by enzymatic digestion is nevertheless preferred over physicochemical treatment as it preserves the structure of the proteins more, and is easier to control. “Enzymatic digestion” means the single or combined action of one or more enzymes in suitable reaction conditions. The enzymes performing proteolysis, called proteases, cut the proteins in specific places. Each protease generally recognizes an amino acid sequence, within which it always makes the same cut. Certain proteases recognize a single amino acid or a sequence of two amino acids between which they perform a cleavage, other proteases only recognize longer sequences. These proteases may be endoproteases or exoproteases. Among the known proteases, we may mention, as described in WO2005/098017:

-   -   specific enzymes such as trypsin which cleaves the peptide bond         at the level of the carboxyl group of the residues Arg and Lys,         endolysin which cleaves the peptide bond of the —CO group of the         lysines, chymotrypsin which hydrolyzes the peptide bond at the         level of the carboxyl group of the aromatic residues (Phe, Tyr         and Trp), pepsin which cleaves the aromatic residues (Phe, Tyr         and Trp) at the level of the NH₂ group, protease V8 of the V8         strain of Staphylococcus aureus which cleaves the peptide bond         at the level of the carboxyl group of the residue GI u;     -   nonspecific enzymes such as thermolysin derived from the         bacterium Bacillus thermoproteolyticus which hydrolyzes the         peptide bond of the NH₂ group of the hydrophobic amino acids         (Xaa-Leu, Xaa-Ile, Xaa-Phe), subtilisin and pronase which are         bacterial proteases which hydrolyze practically all the bonds         and can transform the proteins to oligopeptides in controlled         reaction conditions (concentration of enzyme and reaction time).

Several proteases may be used simultaneously, if their modes of action are compatible, or they may be used successively. In the context of the invention, the sample is preferably digested by the action of a protease enzyme, for example trypsin.

Generation of peptides using a chemical reagent or a protease may be obtained by simple reaction in solution. It may also be carried out with a microwave oven [10], or under pressure [11], or else with an ultrasonic device [12]. In these last three cases, the protocol will be much quicker.

Among the peptides thus obtained, the specific peptides of the protein are called proteotypic peptides. These are the ones that will be determined by mass spectrometry.

According to the invention, the markers of the mechanisms of resistance of bacteria to glycopeptides are proteins of the bacterium in which the mechanisms of resistance to glycopeptides are to be investigated. In particular, said proteins are digested to peptides, preferably by an enzyme, more preferably by trypsin.

Moreover, the sample containing protein markers characterizing mechanisms of bacteria's resistance to glycopeptides may also be treated beforehand for purposes of purification. This preliminary purification treatment may be carried out before or after the step for generating peptides as described above.

The preliminary sample purification treatment is generally known by a person skilled in the art and may notably employ techniques of centrifugation, filtration, electrophoresis or chromatography. These separation techniques may be used alone or combined with one another to obtain multidimensional separation. For example, multidimensional chromatography may be used, combining separation by ion exchange chromatography with reversed-phase chromatography, as described by T. Fortin et al. [13], or H. Keshishian et al. [14]. In these works, the chromatographic medium may be in a column or in a cartridge (solid phase extraction).

The electrophoretic or chromatographic fraction (or retention time in uni- or multidimensional chromatography) of the proteotypic peptides is characteristic of each peptide and application of these techniques therefore makes it possible to select the proteotypic peptide or peptides to be determined. This fractionation of the peptides generated makes it possible to increase the specificity of subsequent determination by mass spectrometry.

An alternative to the techniques of electrophoresis or chromatography for fractionation of the peptides consists of purifying the N-glycopeptides specifically ([15] and patent application WO 2008/066629). However, purification of this kind only allows quantification of the peptides that have undergone a post-translational modification of the N-glycosylation type. Now, not all of the proteins are glycosylated, which therefore limits its use.

The mass spectrometry to be employed in the method of the invention is widely known by a person skilled in the art as a powerful tool for analysis and detection of different types of molecules. In general, any type of molecule that can be ionized can be detected as a function of its molecular weight using a mass spectrometer. Depending on the nature of the molecule to be detected, of protein origin or of metabolic origin, particular technologies of mass spectrometry may be more suitable. Nevertheless, regardless of the method of mass spectrometry used for detection, the latter comprises a step of ionization of the target molecule into so-called molecular ions, in the present case a step of ionization of the characterizing markers, and a step of separation of the molecular ions obtained as a function of their mass.

All mass spectrometers comprise:

-   -   an ionization source for ionizing the markers present in the         sample to be analyzed, i.e. to confer a positive or negative         charge on these markers;     -   a mass analyzer for separating the ionized markers, or molecular         ions, as a function of their mass-to-charge ratio (m/z);     -   a detector for measuring the signal produced either directly by         the molecular ions, or by ions produced from the molecular ions,         as detailed below.

The ionization step necessary for carrying out mass spectrometry may be performed by any method known by a person skilled in the art. The ionization source allows the molecules to be determined to be brought into an ionized gaseous state. An ionization source may be used either in positive mode for studying the positive ions, or in negative mode for studying the negative ions. There are several types of sources and they will be used depending on the result required and the molecules analyzed. We may mention, notably:

-   -   electron ionization (EI), chemical ionization (CI) and         desorption chemical ionization (DCI)     -   fast atom bombardment (FAB), metastable atom bombardment (MAB)         or ion bombardment (SIMS, LSIMS)     -   inductively coupled plasma (ICP)     -   atmospheric pressure chemical ionization (APCI) and atmospheric         pressure photoionization (APPI)     -   electrospray (ESI)     -   matrix-assisted laser desorption/ionization (MALDI),         surface-enhanced desorption/ionization (SELDI) or         desorption/ionization on silicon (DIOS)     -   ionization-desorption by interaction with metastable species         (direct analysis in real time, DART)

Notably, ionization may be carried out as follows: the sample containing the target molecules is introduced into an ionization source, where the molecules are ionized in the gaseous state and thus transformed into molecular ions that correspond to the initial molecules. An ionization source of the electrospray type (ESI, for electrospray ionization) allows a molecule to be ionized while converting it from a liquid state to a gaseous state. The molecular ions obtained then correspond to the molecules present in the liquid state, with, in positive mode, one, two, or even three additional protons or more and are therefore carriers of one, two, or even three charges or more. For example, when the target molecule is a protein, ionization of the proteotypic peptides obtained after fractionation of the target protein, using a source of the electrospray type operating in positive mode, leads to polypeptide ions in the gaseous state, with one, two, or even three additional protons or more and which are therefore carriers of one, two, or even three charges or more, and allows transition from a liquid state to a gaseous state [16]. This type of source is particularly suitable when the target molecules or proteotypic peptides obtained are separated beforehand by reversed-phase liquid chromatography. However, the ionization yield of the molecules present in the sample may vary as a function of the concentration and nature of the different species present. This phenomenon is reflected in a matrix effect that is well known by a person skilled in the art.

A MALDI ionization source will allow molecules to be ionized from a sample in the solid state.

The mass analyzer in which the step of separation of the ionized markers is carried out as a function of their mass/charge ratio (m/z) is any mass analyzer known by a person skilled in the art. We may mention the low-resolution analyzers, of quadrupole (Q), 3D ion trap (IT) or linear type (LIT), also called ion trap analyzers, and the high-resolution analyzers, allowing the exact mass of the analytes to be measured, and which notably use the magnetic sector coupled to an electric sector, time of flight (TOF), Fourier transform ion cyclotron resonance (FT-ICR), Orbitrap.

Separation of the molecular ions as a function of their m/z ratio may be performed once (single mass spectrometry or MS), or else several successive MS separations may be carried out. When two successive MS separations are carried out, the analysis is called MS/MS or MS². When three successive MS separations are carried out, the analysis is called MS/MS/MS or MS³, and more generally, when n successive MS separations are performed, the analysis is called MS^(n).

Among the techniques employing several successive separations, SRM mode (Selected Reaction Monitoring) in the case of detection or assay of a single target molecule, or else MRM mode (Multiple Reaction Monitoring) in the case of detection or assay of several target molecules, are particular applications of MS² separation. Similarly, the MRM³ mode is a particular application of MS/MS/MS separation. This is then called targeted mass spectrometry.

In the case of detection in single MS mode, it is the mass/charge ratio of the molecular ions obtained that is correlated with the target molecule to be detected. In the case of detection in MS/MS mode, essentially two steps are added, relative to MS determination, which are:

-   -   fragmentation of the molecular ions, which are then called         precursor ions, to give ions called first-generation fragment         ions, and     -   separation of the ions called first-generation fragment ions as         a function of their mass (m/z)₂, the ratio (m/z)₁ corresponding         to the (m/z) ratio of the precursor ions.

It is then the mass/charge ratio of the first-generation fragment ions thus obtained that is correlated with the target molecule to be detected. First-generation fragment ion means an ion derived from the precursor ion, following a fragmentation step, and whose mass-to-charge ratio m/z is different from the precursor ion.

The pairs (m/z)₁ and (m/z)₂ are called transitions and are representative of the characteristic ions to be detected.

The characteristic ions that are detected in order to be correlated with the target molecule are selected by a person skilled in the art according to standard methods. Selection of them will advantageously lead to assays that are the most sensitive, the most specific and the most robust as possible, in terms of reproducibility and reliability. In the methods developed for the selection of proteotypic peptides (m/z)₁, and of first-generation fragment (m/z)₂, the choice is essentially based on the intensity of the response. For more detail, reference may be made to V. Fusaro et al. [17]. Commercial software, such as the MIDAS and MRM Pilote software from Applied Biosystems or else MRMaid [18] will be able to be used by a person skilled in the art for predicting all the possible pairs of transitions. It will also be possible to use a database called PeptideAtlas, constructed by F. Desiere et al. [19] for compiling all the MRM transitions of peptides described by the scientific community. This PeptideAtlas database is available with free access on the Internet. For nonprotein molecules, it is also possible to use databases, for example that accessible via the Cliquid software from the company Applied Biosystems (United States of America).

An alternative approach for selecting the proteotypic peptides, (m/z)₁ and (m/z)₂, consists of using the MS/MS fragmentation spectra obtained in other work. This work may be, for example, the stages of discovery and identification of the biomarkers by proteome analysis. This approach was proposed by Thermo Scientific at user conferences [18]. It makes it possible to generate a list of candidate transitions from the peptides identified experimentally with the SIEVE software (Thermo Scientific). Certain criteria have been detailed by J. Mead et al. [18] for selecting the ions (m/z)₁ and (m/z)₂ and are detailed below:

-   -   the peptides with internal cleavage sites, i.e. with internal         lysine or arginine, must be avoided, unless the lysine or         arginine is followed by proline,     -   the peptides with asparagine or glutamine must be avoided as         they may undergo deamination,     -   the peptides with glutamine or glutamic acid at the N-terminus         must be avoided as they may cyclize spontaneously,     -   the peptides with methionine must be avoided as they may undergo         oxidation,     -   the peptides with cysteine must be avoided as they may be         modified nonreproducibly during an optional step of         denaturation, reduction and blocking of the thiol functions,     -   the peptides with proline may be regarded as favorable because         they generally produce intense fragments in MS/MS with a single,         very predominant peak. However, a single very predominant         fragment does not allow validation of the identity of the         transition in a complex mixture. In fact, only the simultaneous         presence of several characteristic fragments makes it possible         to verify that the required precursor ion is in fact detected,     -   the peptides having a proline adjacent to the C-terminus         (position n-1) or in second position relative to the C-terminus         (position n-2) are to be avoided because in this case the size         of first-generation fragment peptide is generally considered to         be too small to be sufficiently specific,     -   selection of fragments having a mass greater than the precursor         is to be preferred, to promote specificity. For this, it is         necessary to select a double-charged precursor ion and select         the most intense first-generation fragment ion having a mass         greater than the precursor, i.e. a single-charged         first-generation fragment ion.

Fragmentation of the selected precursor ions is carried out in a fragmentation cell such as the models of the triple quadrupole type [20], or ion trap type [21], or else of the time of flight (TOF) type [22], which also allow separation of the ions. The fragmentation or fragmentations will be carried out conventionally by collision with an inert gas such as argon or nitrogen, within an electric field, by photo-excitation or photodissociation using an intense light source, collision with electrons or radical species, by application of a potential difference, for example in a time-of-flight tube, or by any other method of activation. The characteristics of the electric field determine the intensity and the nature of fragmentation. Thus, the electric field applied in the presence of an inert gas, for example in a quadrupole, determines the collision energy supplied to the ions. This collision energy will be optimized, by a person skilled in the art, to increase the sensitivity of the transition to be determined. As an example, it is possible to vary the collision energy between 5 and 180 e⁻V in q2 in an AB SCIEX QTRAP® 5500 mass spectrometer from the company Applied Biosystems (Foster City, United States of America). Similarly, the duration of the collision step and the excitation energy within, for example, an ion trap will be optimized, by a person skilled in the art, to lead to the most sensitive determination. As an example, it is possible to vary this duration, dubbed excitation time, between 0.010 and 50 ms and the excitation energy between 0 and 1 (arbitrary unit) in Q3 in an AB SCIEX QTRAP® 5500 mass spectrometer from the company Applied Biosystems. Finally, detection of the selected characteristic ions is performed conventionally, notably using a detector and a processing system. The detector collects the ions and produces an electrical signal whose intensity depends on the quantity of ions collected. The signal obtained is then amplified for processing by computer. A data-processing computer system allows the data received by the detector to be converted to a mass spectrum.

The principle of the SRM mode, or of the MRM mode, is to select a precursor ion specifically, fragment it, and then select one of its fragment ions specifically. For such applications, devices of the triple quadrupole type or ion-trap triple quadrupole hybrids are generally used.

In the case of a triple quadrupole device (Q1q2Q3) used in MS² mode, for determining or detecting a target protein, the first quadrupole (Q1) makes it possible to filter the molecular ions corresponding to the proteotypic peptides characteristic of the protein to be assayed, obtained in a previous digestion step, as a function of their mass-to-charge ratio (m/z). Only the peptides having the mass/charge ratio of the required proteotypic peptide, the ratio called (m/z)₁, are transmitted into the second quadrupole (q2) and play the role of precursor ions for subsequent fragmentation. The q2 analyzer makes it possible to fragment the peptides of mass/charge ratio (m/z)₁ into first-generation fragment ions. Fragmentation is generally obtained by collision of the precursor peptides with an inert gas, such as nitrogen or argon in q2. The first-generation fragment ions are transmitted into a third quadrupole (Q3) which filters the first-generation fragment ions as a function of a specific mass-to-charge ratio, the ratio called (m/z)₂. Only the first-generation fragment ions having the mass/charge ratio of a fragment characteristic of the required proteotypic peptide (m/z)₂ are transmitted into the detector to be detected, or even quantified.

This operating mode displays dual selectivity, in relation to selection of the precursor ion on the one hand and selection of the first-generation fragment ion on the other hand. Mass spectrometry in SRM or MRM mode is therefore advantageous for quantification.

When the mass spectrometry employed in the method of the invention is tandem mass spectrometry (MS², MS³, MS⁴ or MS⁵), several mass analyzers may be coupled together. For example, a first analyzer separates the ions, a collision cell allows the ions to be fragmented, and a second analyzer separates the fragment ions. Certain analyzers, such as ion traps or FT-ICR, constitute several analyzers in one and make it possible to fragment the ions and analyze the fragments directly.

According to preferred embodiments of the invention, the method of the invention comprises one or more of the following characteristics:

-   -   the mass spectrometry employed for the properties of potential         resistance to at least one antimicrobial is spectrometry of the         MS/MS type, which has the advantage of generating a specific         fragment of the molecule to be detected or to be quantified, and         thus of giving the assay method great specificity;     -   the MS/MS spectrometry is MRM spectrometry, which has the         advantage of using an analysis cycle time in the mass         spectrometer of some tens of milliseconds, which makes it         possible to detect or quantify with great sensitivity, in a         multiplexed fashion, a large number of different molecules;     -   if applicable, determination of the typing properties, and of         the virulence factor is employed in the same mass spectrometry         apparatus as determination of the markers of resistance to at         least one antimicrobial, preferably simultaneously, which has         the advantage of reducing the analysis times and the equipment         cost; this also facilitates processing and presentation of the         results.

Besides determination of the resistance to an antibiotic, it is appropriate to identify the microorganism or microorganisms present in the test sample.

The methods of identification of microorganisms are widely known by a person skilled in the art, as described for example by Murray P. R. et al. in Manual of Clinical Microbiology, 2007, 9th edition, and in particular in Vol. I, Section III, chapters 15 and 16 for bacteria and yeasts, Vol. II, Section VI, chapter 82 for viruses, and Vol. II, Section X, chapter 135 for protozoa. As examples of classical methods of identification, we may mention determination of the biological profile, using for example the Vitek 2 identification cards (bioMérieux™), or else using techniques of molecular biology with identification criteria based on investigation for the presence of certain genes, and investigation of their sequence. Identification may be carried out directly from the sample in which the identification is being effected, or else the microorganisms contained in the sample may be cultured by methods that are familiar to a person skilled in the art with optimal culture media and culture conditions adapted in relation to the species of microorganisms to be investigated, as described by Murray P. R. et al. in Manual of Clinical Microbiology, 2007, 9th edition, Vol. I, Section III, chapter 14, and in particular in Vol. I, Section IV, chapter 21 for bacteria, Vol. II, Section VI, chapter 81 for viruses, Vol. II, Section VIII, chapter 117 for yeasts, and Vol. II, Section X, chapter 134 for protozoa.

Thus, generally, in the case of identification of a bacterium in a sample by a biochemical method, it is first necessary to obtain it in culture pure, for example after seeding on agar. Molecular biology (PCR) may in certain cases be applied directly to the sample to be analyzed.

Instead of culturing the microorganisms, the latter may be concentrated by direct capture in the sample by means of active surfaces. Such a method has been described by W.-J. Chen et al. [10], who captured various bacterial species using magnetic beads with a surface activated with Fe₃O₄/TiO₂. Capture by other means is also possible, such as capture by lectins [23], or by antibodies [24], or by vancomycin [25]. Capture makes it possible to concentrate the microorganisms and thus reduce or even eliminate the culture step. This results in a considerable saving of time.

Identification may also be carried out by mass spectrometry, according to the techniques described above, preferably by MS, by MS/MS, or else by MS followed by spectrometry of the MS/MS type, which constitutes one embodiment of the invention. In this case as well, the sample may be submitted beforehand to a culture step such as seeding on agar.

Use of a method of identification by MS is advantageous in that it can be carried out in a few minutes and in that it requires a mass spectrometer with a single analyzer, i.e. an instrument that is less complex than a tandem mass spectrometer used in MS/MS.

Use of a method of identification by MS followed by spectrometry of the MS/MS type is also advantageous. It provides assurance of the identity of the ions observed in MS, which increases the specificity of the analysis.

Use of a method of identification by MS/MS of the MRM type has the advantage of being more sensitive and simpler than the approaches MS then traditional MS/MS. This method does not require powerful software, which is necessary for processing information between acquisition of the MS spectrum and of the MS/MS spectrum, and does not require resetting of the machine variables, necessary for the succession of MS and then MS/MS spectra.

The method of identification by MS may be carried out with an electrospray source on a raw sample, as described by S. Vaidyanathan et al. [26] or by R. Everley et al. [27] after chromatographic separation. Different m/z ranges then allow the microorganisms to be identified. S. Vaidyanathan et al. used a window between 200 and 2000 Th, and R. Everley et al. used a window between 620 and 2450 Th. The mass spectra may also be deconvoluted to find the mass of the proteins independently of their state of charge. R. Everley et al. thus exploited masses between about 5000 and 50 000 Da. Alternatively, the method of identification by MS may also be carried out using MALDI-TOF, as described by Claydon et al. [3] and T. Krishnamurthy and P. Ross [4]. Analysis combines acquisition of a mass spectrum and interpretation by expert software. It is extremely simple and can be performed in a few minutes. This method of identification is currently being adopted in medical analysis laboratories [5].

Identification of bacteria by MS and then MS/MS via their proteins present in the sample has been widely applied by many teams. As an example, we may cite the recent works of Manes N. et al. [28], who studied the peptidome of Salmonella enterica, or the works of R. Nandakumar et al. [29] or of L. Hernychova et al. [30], who studied the proteome of bacteria after digestion of the proteins with trypsin. The classical approach consists of i) acquiring an MS spectrum, ii) successively selecting each precursor ion observed on the MS spectrum with a strong signal, iii) successively fragmenting each precursor ion and acquiring its MS/MS spectrum, iv) interrogating protein databases such as SWISS-PROT or NCBI, using software such as Mascot (Matrix Science, London, United Kingdom) or SEQUEST (Thermo Scientific, Waltham, United States of America), to identify the peptide having a high probability of corresponding to the MS/MS spectrum observed. This method may lead to identification of a microorganism if a protein or a peptide characteristic of the species is identified.

One of the advantages of using mass spectrometry is that it is particularly useful for quantifying molecules, in the present case the markers of the mechanisms of resistance of bacteria to the glycopeptides. For this purpose, the current intensity detected is used, which is proportional to the quantity of the target molecule. The current intensity thus measured can serve as a quantitative measure for determining the quantity of target molecule present, which is characterized by expression in units of the International System (Système International, SI) of the type mol/m³ or kg/m³, or by multiples or submultiples of these units, or by the usual derivatives of the SI units, including their multiples or submultiples. As a nonlimiting example, units such as ng/ml or fmol/l are units characterizing a quantitative measurement.

However, calibration is necessary so as to be able to correlate the measured peak area, corresponding to the current intensity induced by the ions detected, with the quantity of the assayed target molecule. For this, the calibrations conventionally used in mass spectrometry can be used in the context of the invention. MRM assays are conventionally calibrated using external standards or, preferably, using internal standards as described by T. Fortin et al. [13]. In the case when the target molecule is a proteotypic peptide, allowing assay of a protein of interest, the correlation between the quantitative measurement and the quantity of target proteotypic peptide, and then the protein of interest, is obtained by calibrating the measured signal relative to a standard signal for which the quantity to be assayed is known. Calibration may be performed by means of a calibration curve, for example obtained by successive injections of standard proteotypic peptide at different concentrations (external calibration), or preferably by internal calibration using a heavy peptide, as internal standard, for example according to the AQUA, QconCAT or PSAQ methods detailed below. “Heavy peptide” means a peptide corresponding to the proteotypic peptide, but in which one or more atoms of carbon 12 (¹²C) is (are) replaced with carbon 13 (¹³C), and/or one or more atoms of nitrogen 14 (¹⁴N) is (are) replaced with nitrogen 15 (¹⁵N).

The use of heavy peptides, as internal standards (AQUA), was also proposed in patent application US 2004/0229283. The principle is to synthesize proteotypic peptides artificially with amino acids comprising isotopes heavier than the usual natural isotopes. Amino acids of this kind are obtained, for example, by replacing some of the atoms of carbon 12 (¹²C) with carbon 13 (¹³C), or by replacing certain of the atoms of nitrogen 14 (¹⁴N) with nitrogen 15 (¹⁵N). The artificial peptide (AQUA) thus synthesized has strictly the same physicochemical properties as the natural peptide (except for a higher mass). It is generally added, at a given concentration, to the sample, upstream of assay by mass spectroscopy, for example between the treatment leading to cleavage of the proteins of the sample of interest and fractionation of the peptides obtained after the treatment step. Accordingly, the AQUA peptide is co-purified with the natural peptide to be assayed, during fractionation of the peptides. The two peptides are therefore injected simultaneously into the mass spectrometer, for assay. They are then subjected to the same ionization yields in the source. Comparison of the peak areas of the natural peptides and AQUA peptides, whose concentration is known, makes it possible to calculate the concentration of the natural peptide and thus arrive at the concentration of the protein to be assayed. A variant of the AQUA technique was proposed by J.-M. Pratt et al. [31] under the name QconCat. This variant is also described in patent application WO 2006/128492. It consists of concatenating various AQUA peptides and of producing the artificial polypeptide in the form of heavy recombinant protein. The recombinant protein is synthesized with amino acids comprising heavy isotopes. In this way it is possible to obtain a standard for calibrating the simultaneous assay of several proteins at lower cost. The QconCAT standard is added at the very start, upstream of the treatment leading to cleavage of the proteins and before the steps of fractionation of the proteins, denaturation, reduction and then blocking the thiol functions of the proteins, if the latter are present. The QconCAT standard therefore undergoes the same cycle of treatment leading to cleavage of the proteins as the natural protein, which makes it possible to take account of the yield of the treatment step leading to cleavage of the proteins. In fact, the treatment, notably by digestion, of the natural protein may not be complete. In this case the use of an AQUA standard would lead to underestimating the quantity of natural protein. For an absolute assay, it may therefore be important to take into account the yields of treatment leading to cleavage of the proteins. However, V. Brun et al. [33] showed that sometimes the QconQAT standards did not reproduce exactly the yield of treatment notably by digestion of the natural protein, without doubt owing to a three-dimensional conformation different from the QconCAT protein. V. Brun et al. [32] then proposed using a method dubbed PSAQ and described in patent application WO 2008/145763. In this case, the internal standard is a recombinant protein, having the same sequence as the natural protein but synthesized with heavy amino acids. The synthesis is carried out ex vivo with heavy amino acids. This standard has strictly the same physicochemical properties as the natural protein (except for a higher mass). It is added at the very start, before the step of fractionation of the proteins, when the latter is present. It is therefore co-purified with the native protein, during the step of fractionation of the proteins. It displays the same yield of treatment, notably by digestion, as the native protein. The heavy peptide obtained after cleavage is also co-purified with the natural peptide, if a step of fractionation of the peptides is carried out. The two peptides are therefore injected simultaneously into the mass spectrometer, to be assayed quantitatively. They are then subjected to the same ionization yields in the source. Comparison of the peak areas of the natural peptides and reference peptides in the PSAQ method makes it possible to calculate the concentration of the protein to be assayed taking into account all of the steps of the assay procedure.

All of these techniques, namely AQUA, QconCAT or PSAQ or any other calibration technique used in assays by mass spectrometry and in particular in MRM or MS assays, can be used for performing the calibration, in the context of the invention.

Preferably, the mass spectrometry used in the method of detection according to the invention is of the MS/MS type. More preferably, the mass spectrometry is MRM.

The method of the invention allows detection of resistances to glycopeptides, characterized by the detection of at least one peptide as resistance marker. Preferably, the method according to the invention makes it possible to detect at least one marker of resistance to vancomycin.

According to a first embodiment, the method according to the invention allows direct detection of resistance to a glycopeptide, without bringing the microorganism potentially present in the sample into contact with said glycopeptide, i.e. without a step of induction of said resistance.

According to another embodiment, the method of the invention comprises an additional step, prior to the detection step, consisting of induction of the mechanism of resistance by bringing said sample into contact with said glycopeptide(s).

Preferably, said resistance marker is a peptide derived from the proteins of the Van type, such as the respective variants of type Van A, Van B, Van C, Van D, Van E, Van G, Van L, Van M and Van N.

According to one embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanA, is characterized by the detection of at least one peptide belonging to the protein VanA and its different variants of sequences SEQ ID No. 1 to SEQ ID No. 4.

SEQ ID No. 1: MKKPLKTVWILKGDRSMNRIKVAILFGGCSEEHDVSVKSAIEIAANI NKEKYEPLYIGITKSGVWKMCEKPCAEWENDNCYSAVLSPDKKMHGL LVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQ SSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKP ARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAV LGNSAALWGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAE ERGRIQETAKKIYKALGCRGLARVDMFLQDNGRIVLNEVNTLPGFTS YSRYPRMMAAAGIALPELIDRLIVLALKG SEQ ID No. 2: MNRIKVAILFGGCSEEHDVSLKSAIEIAANINKEKYEPLYIGITKSG VWKMCEKPCAEWENDNCYSAVLSPDKKMHGLLVKKNHEYEINHVDVA FSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAK NAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSAD ELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIR LQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETAKKIYKA LGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRMMAAAGIAL PELIDRLIVLALKG SEQ ID No. 3: MNRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSG VWKMCEKPCAEWENDNCYSAVLSPDKKMHGLLVKKNHEYEINHVDVA FSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAK NAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSAD ELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALAVGEVDQIR TAKKIYKALGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRM MAAAGIALPELIDRLIVLALKG SEQ ID No. 4: MNRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSG VWKMCEKPCAEWENDNCYSAVLSPDKKMHGLLVKKNHEYEINHVDVA FSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAK NAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSAD ELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIR LQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETAKKIYKA LGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRMMAAAGIAL PELIDRLIVLALKG said peptides of type VanA preferably being selected from the peptides of sequence SEQ ID No. 5 to SEQ ID No. 16 as defined below:

Peptide Amino Position of the SEQ ID acid peptide in the VanA No. sequence protein or proteins SEQ ID IHQEVEPEK 243-251 for the proteins of SEQ No. 2, 3, No. 5 4; 259-267 for the protein of sequence SEQ ID No. 1 SEQ ID LIVLALK 336-342 for the proteins of SEQ No. 2, 3, No. 6 4; 352-358 for the protein of sequence SEQ ID No. 1 SEQ ID LQYGIFR 236-242 for the proteins of SEQ No. 2, 3, No. 7 4; 252-258 for the protein of sequence SEQ ID No. 1 SEQ ID MHGLLVK 75-81 for the proteins of SEQ No. 2, 3, 4; No. 8 91-97 for the protein of sequence SEQ ID No. 1 SEQ ID MMAAAGIALPELIDR 321-335 for the proteins of SEQ No. 2, 3, No. 9 4; 337-351 for the protein of sequence SEQ ID No. 1 SEQ ID NAGIATPAFWVINK 142-155 for the proteins of SEQ No. 2, 3, No. 10 4; 158-171 for the protein of sequence SEQ ID No. 1 SEQ ID SAIEIAANINK 23-33 for the proteins of SEQ No. 2, 3, 4; No. 11 39-49 for the protein of sequence SEQ ID No. 1 SEQ ID SGSSFGVK 175-182 for the proteins of SEQ No. 2, 3, No. 12 4; 191-198 for the protein of sequence SEQ ID No. 1 SEQ ID SLTYIVAK 134-141 for the proteins of SEQ No. 2, 3, No. 13 4; 150-157 for the protein of sequence SEQ ID No. 1 SEQ ID VDMFLQDNGR 291-300 for the proteins of SEQ No. 2, 3, No. 14 4; 307-316 for the protein of sequence SEQ ID No. 1 SEQ ID VNSADELDYAIESAR 184-198 for the proteins of SEQ No. 2, 3, No. 15 4; 200-214 for the protein of sequence SEQ ID No. 1 SEQ ID YEPLYIGITK 36-45 for the proteins of SEQ No. 2, 3, 4; No. 16 52-61 for the protein of sequence SEQ ID No. 1

Advantageously, the markers of type VanA selected from the peptides of sequence SEQ ID No. 5 to SEQ ID No. 16 are detected after induction of the mechanism of resistance.

Advantageously, the markers of type VanA selected from the peptides of sequence SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 15 and SEQ ID No. 16 are detected without an induction step.

According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanB, is characterized by the detection of at least one peptide belonging to the protein VanB and its different variants of sequences SEQ ID No. 17 to SEQ ID No. 28.

SEQ ID No. 17: MNKIKVAIIFGGCSEEHDVSVKSAIEIAANINTEKFDPHYIGITKNGVWKLCKKPCTEW EADSLPAIFSPDRKTHGLLVMKEREYETRRIDVAFPVLHGKCGEDGAIQGLFELSGIP YVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIEKGDKPEARTLTYPVFVKPARSG SSFGVTKVNSTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVMGNEDDLIVGEVDQIR LSHGIFRIHQENEPEKGSENAMIIVPADIPVEERNRVQETAKKVYRVLGCRGLARVD LFLQEDGGIVLNEVNTLPGFTSYSRYPRMAAAAGITLPALIDSLITLAIER SEQ ID No. 18: MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FELSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTY PVFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVM GNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQET AKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMMAAAGITL PALIDSLITLALKR SEQ ID No. 19: MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQIIDKGDKPEAGALTYP VFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVMG NEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQETA KKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTMPGFTSYSRYPRMVAAAGITLP ALIDSLITLALKR SEQ ID No. 20: MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQIIDKGDKPEAGALTYP VFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVMG NEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQETA KKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTMPGFTSYSRYTRMVAAAGITLP ALIDSLITLALKR SEQ ID No. 21: MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTY PVFVKPARSGSSFGLTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVM GNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQET AKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMMAAAGITL PALIDSLITLALKR SEQ ID No. 22: MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTY PVFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVM GNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQET AKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMMAAAGITL PALIDSLITLALKR SEQ ID No. 23: MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FVLSGIPYVGCDIQSSAVCMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTY PVFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVM GNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQET AKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMVAAAGITL PALIDSLITLALKR SEQ ID No. 24: MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGGGEDGAIQ GLFVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGAL TYPVFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAV MGNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQE TAKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMMAAAGIT LPALIDSLITLALKR SEQ ID No. 25: MNRIKVAIIFGGCSEEHDVSVKSAIEIAANINTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FELSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTY PVFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVM GNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQET AKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMVAAAGITL PALIDSLITLALKR SEQ ID No. 26: MNRIKVATIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTY PVFVKPARAGSSFGLTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVM GNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQET AKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMMAAAGITL PALIDSLITLALKR SEQ ID No. 27: MNRIKVATIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTY PVFVKPARSGSSFGLTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVM GNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQET AKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMMAAAGITL PAMIDSLITLALKR SEQ ID No. 28: MNRIKVATIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPC TEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGL FVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTY PVFVKPARSGSSFGVTKVNGPEELNAAIEAAGQYDGKILIEQAISGCEVGCAVM GNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQET AKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTMPGFTSYSRYPRMVAAAGITL PALIDSLITLALKR said markers of type VanB preferably being selected from the peptides of sequence SEQ ID No. 29 to SEQ ID No. 35 as defined below:

Peptide Amino Position of the SEQ ID acid peptide in the VanB No. sequence protein or proteins SEQ ID FDPHYIGITK 36-45 for the proteins of SEQ No. 17, 18, No. 29 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 SEQ ID IDVAFPVLHGK 90-100 for the proteins of SEQ No. 17, 18, No. 30 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 SEQ ID IHQENEPEK 242-250 for the proteins of SEQ No. 17, No. 31 18, 19, 20, 21, 22, 23, 25, 26, 27, 28; 244- 252 for the protein of sequence SEQ ID No. 24 SEQ ID LSHGIFR 235-241 for the proteins of SEQ No. 17, No. 32 18, 19, 20, 21, 22, 23, 25, 26, 27, 28; 237- 243 for the protein of sequence SEQ ID No. 24 SEQ ID SLAYILTK 133-140 for the proteins of SEQ No. 17, No. 33 18, 19, 20, 21, 22, 23, 25, 26, 27, 28; 135- 142 for the protein of sequence SEQ ID No. 24 SEQ ID THGLLVMK 74-81 for the proteins of SEQ No. 17, 18, No. 34 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 SEQ ID VQETAK 271-276 for the proteins of SEQ No. 17, No. 35 18, 19, 20, 21, 22, 23, 25, 26, 27, 28; 273- 278 for the protein of sequence SEQ ID No. 24

Advantageously, the markers of type VanB selected from the peptides of sequence SEQ ID No. 29, SEQ ID No. 30, SEQ ID No. 32 and SEQ ID No. 33 are detected after induction of the mechanism of resistance.

According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanC, is characterized by the detection of at least one peptide belonging to the protein VanC and its different variants of sequences SEQ ID No. 36 to SEQ ID No. 58. Notably the variants VanC1 are characterized by the detection of at least one peptide belonging to the protein VanC1 and its different variants of sequences SEQ ID No. 36 to SEQ ID No. 43, the variants VanC2 or VanC3 are characterized by the detection of at least one peptide belonging to the protein VanC2 or Van C3 and its different variants of sequences SEQ ID No. 46 to SEQ ID No. 51 and SEQ ID No. 53 to SEQ ID No. 57, the variants VanC4 are characterized by the detection of at least one peptide belonging to the protein VanC4 and its different variants of sequences SEQ ID No. 44, SEQ ID No. 45, SEQ ID No. 52 and SEQ ID No. 58

SEQ ID No. 36: MKKIAVLFGGNSPEYSVSLASAASVIQAIDPLKYEVMTIGIAPTMDWYLYQGNLANVRND TWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQGLLELMNLPYVGCH VAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATIDRFIQDHGFPIFIKPNEA GSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIGCGILGNEQLTIGACDA ISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQLLYRNLGLTGLARIDF FVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILVEQLIALAEEDKR SEQ ID No. 37: MKKIAVLFGGNSPEYSVSLASAASVIQAIDPLKYEVMTIGIAPTMDWYWYQGNL ANVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQGL LELMNLPYVGCHVAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATIDR FIQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIGC GILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQLL YRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILVE QLIALAEEDKR SEQ ID No. 38: MKKIAVLFGGNSPEYSVSLASAASVIQAIDPLKYEVMTIGIAPTMDWYWYQGNL ANVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQGL LELMNLPYVGCHVAATALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATIDR FIQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIGC GILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQLL YRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILVE QLIALAEEDKR SEQ ID No. 39: MKKIAVLFGGNSPEYSVSLTSAASVIQAIDPLKYEVMTIGIAPTMDWYWYQGNLA NVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQGLL ELMNLPYVGCHVAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATIDRF IQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIGC GILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQLL YRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILVE QLIALAEEDKR SEQ ID No. 40: MKKIAVLFGGNSPEYSVSLTSAASVIQAIDPLKYEVMTIGIAPTMDWYWYQGNLA NVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQGLL ELMNLPYVGCHVAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATIDRF IQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIGC GILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQLL YRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILVE KLIALAEEDKR SEQ ID No. 41: MKKIAVLFGGNSPEYSVSLTSAESVIQAINPLKYEVMTIGIAPTMDWYWYQGNLA NVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQGLL ELMNLPYVGCHVAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATIDRF IQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIGC GILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQLL YRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILVE QLIALAEEDKR SEQ ID No. 42: MMKKIAVLFGGNSPEYSVSLASAASVIQAIDPLKYEVMTIGIAPTMDWYWYQGN LANVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQG LLELMNLPYVGCHVAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATID RFIQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIG CGILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQL LYRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILV EQLIALAEEDKR SEQ ID No. 43: MMKKIAVLFGGNSPEYSVSLTSAASVIQAIDPLKYEVMTIGIAPTMDWYWYQGN LANVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQG LLELMNLPYVGCHVAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATID RFIQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIG CGILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQL LYRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILV EQLIALAEEDKR SEQ ID No. 44: MKKIAIIFGGNSPEYAVSLASATSAIEALQSSPDDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEAQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAASALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QDQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQK NIAGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIET KVKEQAQLLYHSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAA IGLSYQELLQKLLVLAKEEVK SEQ ID No. 45: MKKIAIIFGGNSPEYAVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAASALCMNKWLLHQAAEAIGVQSAPTILLTNQDNQ QRQIEAFIQTHDFPVFFKPNEAGSSKGITKVTCVEEIAPALKEAFAYCSAVLLQK NIAGVEIGCGILGNDSLTVGACDAISLVEGFFDFEEKYQLISAKITVPAPLPETIET KVKEQAQLLYHSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAA IGLSYQELLQKLLVLAKEEGK SEQ ID No. 46: MKKIAIIFGGNSPEYAVSLASATSALEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IAGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLVLAKEEVK SEQ ID No. 47: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IAGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLVLAKEEVK SEQ ID No. 48: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IAGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTERGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLVLAKEEVK SEQ ID No. 49: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IVGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLVLAKEEVK SEQ ID No. 50: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVASSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IVGVEIGCGILGNDSLTVGACDAISLEDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLILAKEEVK SEQ ID No. 51: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHTQKIKPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGEDG SIQGLFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQQ EQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKNI AGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIETKV KEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAVG LSYQELLQKLLVLAKEEVK SEQ ID No. 52: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHTQKIQPLFEGNGFWISEAQQTLVPDVLFPIMHGKYGEDG SIQGMFELMKLPYVGCGVAASALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QRQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIAPALKEAFAYCSAVLLQK NIAGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIET KVKEQAQLLYHSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAA VGLSYQELLQKLLVLAKEEGK SEQ ID No. 53: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKQKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNHANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IAGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLVLAKEEVK SEQ ID No. 54: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKQKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVASSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IVGVEIGCGILGNDSLTVGACDAISLEDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLILAKEEVK SEQ ID No. 55: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKQKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGMFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNHAN QQEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQ KNIAGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIE TKVKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMA AVGLSYQELLQKLLVLAKEEVK SEQ ID No. 56: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGITPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IAGVEIGCGILGNDSLTVGACDAISLVDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLVLAKEEVK SEQ ID No. 57: MKKIAIIFGGNSPEYTVSLASATSAIEALQSSPYDYDLSLIGITPDAMDWYLYTGE LENIRQDTWLLDTKHKQKIQPLFEGNGFWLSEEQQTLVPDVLFPIMHGKYGED GSIQGLFELMKLPYVGCGVAGSALCMNKWLLHQAAAAIGVQSAPTILLTNQANQ QEQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIASALKEAFTYCSAVLLQKN IVGVEIGCGILGNDSLTVGACDTISLVDGFFDFEEKYQLISAKITVPAPLPETIETK VKEQAQLLYRSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAV GLSYQELLQKLLVLAKEEVK SEQ ID No. 58: MKKIAIIFGGNSSEYTVSLASATSAIEALQSSPYDYDLSLIGIAPDAMDWYLYTGE LENIRQDTWLLDTKHTQKIQPLFEENGFWLSEAQQTLVPDVLFPIMHGKYGEDG SIQGLFELMKLPYVGCGVAASALCMNKWLLHQAAAAIGVQSAPTILLTNQDNQQ QQIEAFIQTHGFPVFFKPNEAGSSKGITKVTCVEEIAPALKEAFAYCSAVLLQKNI AGVEIGCGILGNDSLTVGACDAISLVEGFFDFEEKYQLISAKITVPAPLPETIETKV KEQAQLLYHSLGLKGLARIDFFVTDQGELYLNEINTMPGFTSHSRYPAMMAAIG LSYQELLQKLLVLAKEEGK said markers of type VanC preferably being selected from the peptides of sequence SEQ ID No. 59 to SEQ ID No. 71 as defined below:

Peptide SEQ ID Amino acid Position of the peptide in the VanC protein No sequence or proteins SEQ ID EQAQLLYR 279-286 for the proteins of SEQ No. 46, 47, 48, 49, No. 59 50, 51, 53, 54, 55, 56, 57; 272-279 for the protein of sequence SEQ ID No. 36; 272-279 for the protein of sequence SEQ ID No. 37; 272-279 for the protein of sequence SEQ ID No. 38; 272-279 for the protein of sequence SEQ ID No. 39; 272-279 for the protein of sequence SEQ ID No. 40; 272-279 for the protein of sequence SEQ ID No. 41; 273-280 for the protein of sequence SEQ ID No. 42; 273-280 for the protein of sequence SEQ ID No. 43 SEQ ID FIQDHGFPIFIKPN 164-183 for the proteins of SEQ No. 42, 43; 163-182 No. 60 EAGSSK for the protein of sequence SEQ ID No. 36; 163-182 for the protein of sequence SEQ ID No. 37; 163-182 for the protein of sequence SEQ ID No. 38; 163-182 for the protein of sequence SEQ ID No. 39; 163-182 for the protein of sequence SEQ ID No. 40; 163-182 for the protein of sequence SEQ ID No. 41 SEQ ID IVPDVLFPVLHG 87-99 for the proteins of SEQ No. 42, 43; 86-98 for No. 61 K the protein of sequence SEQ ID No. 36; 86-98 for the protein of sequence SEQ ID No. 37; 86-98 for the protein of sequence SEQ ID No. 38; 86-98 for the protein of sequence SEQ ID No. 39; 86-98 for the protein of sequence SEQ ID No. 40; 86-98 for the protein of sequence SEQ ID No. 41 SEQ ID NCHQLTFSSQGFI 69-85 for the proteins of SEQ No. 42, 43; 68-84 for No. 62 LGEK the protein of sequence SEQ ID No. 36; 68-84 for the protein of sequence SEQ ID No. 37; 68-84 for the protein of sequence SEQ ID No. 38; 68-84 for the protein of sequence SEQ ID No. 39; 68-84 for the protein of sequence SEQ ID No. 40; 68-84 for the protein of sequence SEQ ID No. 41 SEQ ID NDTWLEDHK 60-68 for the proteins of SEQ No. 42, 43; 59-67 for No. 63 the protein of sequence SEQ ID No. 36; 59-67 for the protein of sequence SEQ ID No. 37; 59-67 for the protein of sequence SEQ ID No. 38; 59-67 for the protein of sequence SEQ ID No. 39; 59-67 for the protein of sequence SEQ ID No. 40; 59-67 for the protein of sequence SEQ ID No. 41 SEQ ID NLGLTGLAR 281-289 for the proteins of SEQ No. 42, 43; 280-288 No. 64 for the protein of sequence SEQ ID No. 36; 280-288 for the protein of sequence SEQ ID No. 37; 280-288 for the protein of sequence SEQ ID No. 38; 280-288 for the protein of sequence SEQ ID No. 39; 280-288 for the protein of sequence SEQ ID No. 40; 280-288 for the protein of sequence SEQ ID No. 41 SEQ ID TALQSALTTAFA 192-212 for the proteins of SEQ No. 42, 43; 191-211 No. 65 YGSTVLIQK for the protein of sequence SEQ ID No. 36; 191-211 for the protein of sequence SEQ ID No. 37; 191-211 for the protein of sequence SEQ ID No. 38; 191-211 for the protein of sequence SEQ ID No. 39; 191-211 for the protein of sequence SEQ ID No. 40; 191-211 for the protein of sequence SEQ ID No. 41 SEQ ID WLLHQLADTMG 132-153 for the proteins of SEQ No. 42, 43; 131-152 No. 66 IASAPTLLLSR for the protein of sequence SEQ ID No. 36; 131-152 for the protein of sequence SEQ ID No. 37; 131-152 for the protein of sequence SEQ ID No. 38; 131-152 for the protein of sequence SEQ ID No. 39; 131-152 for the protein of sequence SEQ ID No. 40; 131-152 for the protein of sequence SEQ ID No. 41 SEQ ID YENDPATIDR 154-163 for the proteins of SEQ No. 42, 43; 153-162 No. 67 for the protein of sequence SEQ ID No. 36; 153-162 for the protein of sequence SEQ ID No. 37; 153-162 for the protein of sequence SEQ ID No. 38; 153-162 for the protein of sequence SEQ ID No. 39; 153-162 for the protein of sequence SEQ ID No. 40; 153-162 for the protein of sequence SEQ ID No. 41 SEQ ID YQLISATITVPAP 250-272 for the proteins of SEQ No. 42, 43; 249-271 No. 68 LPLALESQIK for the protein of sequence SEQ ID No. 36; 249-271 for the protein of sequence SEQ ID No. 37; 249-271 for the protein of sequence SEQ ID No. 38; 249-271 for the protein of sequence SEQ ID No. 39; 249-271 for the protein of sequence SEQ ID No. 40; 249-271 for the protein of sequence SEQ ID No. 41 SEQ ID ITVPAPLPETIET 263-276 for the proteins of SEQ No. 44, 45, 46, 47, No. 69 K 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 SEQ ID QDTWLLDTK 62-70 for the proteins of SEQ No. 44, 45, 46, 47, 48, No. 70 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 SEQ ID YQLISAK 256-262 for the proteins of SEQ No. 44, 45, 46, 47, No. 71 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58

According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanD, is characterized by the detection of at least one peptide belonging to the protein VanD and its different variants of sequences SEQ ID No. 72 to SEQ ID No. 79.

SEQ ID No. 72: MFKIKVAVLFGGCSEEHNVSIKSAMEIAANIDTKKYQPYYIGITKSGVWK MCEKPCLEWEQYAGDPVVFSPDRSTHGLLIQKDKGYEIQPVDVVLPMIHG KFGEDGSIQGLLELSGIPYVGCDIQSSVTCMDKALAYTVVKNAGIAVPGF RILQEGDRLETEDFVYPVFVKPARSGSSFGVNKVCKAEELQAAIEEARKY DSKILIEEAVTGSEVGCAILGNGNDLMAGEVDQIELRHGFFKIHQEAQPE KGSENAVIRVPAALPDEVRERIQKTAMKIYRILGCRGLARIDLFLREDGC IVLNEVNTMPGFTSYSRYPRMMTAAGFTLTEILDRLIELSLRR SEQ ID No. 73: MFKIKVAVLFGGCSEEHNVSIKSAMEIAANIDTKKYQPYYIGITKSGVWK MCEKPCLGWEQYAGDPVVFSPDRSTHGLLIQKDTGYEIQPVDVVFPMIHG KFGEDGSIQGLLELSGIPYVGCDIQSSVICMDKALAYTVVKNAGIAVPGF RILQEGDRLETEDLVYPVFVKPARSGSSFGVNKVCKAEELQAAIREARKY DSKILIEEAVTGSEVGCAILGNENDLMAGEVDQIELRHGFFKIHQEAQPE KGSENAVIRVPAALPDEVRERIRKTAMKIYRILGCRGLARIDLFLREDGC IVLNEVNTMPGFTSYSRYPRMMTAAGFTLSEILDRLIEFSLRR SEQ ID No. 74: MFRIKVAVLFGGCSEEHNVSIKSAMEIAANIDTKKYQPYYIGITKSGVWK MCEKPCLEWEQYAGDPVVFSPDRSTHGLLIQKDKGYEIQPVDVVFPMIHG KFGEDGSIQGLLELSGIPYVGCDIQSSVICMDKALAYTVVKNAGITVPGF RILQEGDRLETEDFVYPVFVKPARSGSSFGVNKVCKAEELQAAIEEARKY DSKILIEEAVTGSEVGCAILGNGNDLMAGEVDQIELRHGFFKIHQEAQPE KGSENAVIRVPAALPDEVREQIQETAMKIYRILGCRGLARIDLFLREDGC IVLNEVNTMPGFTSYSRYPRMMTAAGFTLSEILDRLIELSLRR SEQ ID No. 75: MFRIKVAVLFGGCSEEHNVSIKSAMEIAANIDTKKYQPYYIGITKSGVWK MCEKPCLEWEQYAGDPVVFSPDRSTHGLLIQKDTGYEIQPVDVGLPMIHG KFGEDGSIQGLLELSGIPYVGCDIQSSVTCMDKALAYTVVKNAGIAVPGF RILQEGDRLETEDFVYPVFVKPARSGSSFGVNKVCKAEELQAAIEDARKY DSKILIEEAVTGSEVGCAILGNGNDLMAGEVDQIELRHGFFKIHQEAQPE KGSENAVIRVPAALPDEVIERIQKTAMKIYRILGCRGLARIDLFLREDGC IVLNEVNTMPGFTSYSRYPRMMTAAGFTLTEILDRLIELSLRR SEQ ID No. 76: MYKLKIAVLFGGCSEEHDVSVKSAMEVAANINKEKYQPFYIGITKSGAWK LCDKPCRDWENYAGYPAVISPDRRIHGLLIQKDGGYESQPVDVVLPMIHG KFGEDGTIQGLLELSGIPYVGCDIQSSVICMDKSLAYMVVKNAGIEVPGF RVLQKGDSLEAETLSYPVFVKPARSGSSFGVNKVCRAEELQAAVTEAGKY DSKILVEEAVSGSEVGCAILGNGNDLITGEVDQIELKHGFFKIHQEAQPE KGSENAVIRVPAALPDEVREQIQETAKKIYRVLGCRGLARIDLFLREDGS IVLNEVNTMPGFTSYSRYPRMMTAAGFTLSEILDRLIGLSLRR SEQ ID No. 77: MYKLKIAVLFGGCSEEHDVSVKSAMEVAANINKEKYQPFYIGITKSGAWK LCDKPCRDWENYAGYPAVISPDRRIHGLLIQKDGGYESQPVDVVLPMIHG KFGEDGTIQGLLELSGIPYVVCDIQSSVICMDKSLAYMVVKNAGIEVPGF RVLQKGDSLEAETLSYPVFVKPARSGSSFGVNKVCRAEELQAAVTEAGKY DSKILVEEAVSGSEVGCAILGNGNDLITGEVDQIELKHGFFKIHQEAQPE KGSENAVIRVPAALPDEVREQIQETAKKIYRVLGCRGLARIDLFLREDGS IVLNEVNTMPGFTSYSRYPRMMTAAGFTLSEILDRLIGLSLRR SEQ ID No. 78: MYKLKIAVLFGGCSEEHDVSVKSAMEVAANINKEKYQPFYIGITKSGAWK LCDKPCRDWENYAGYPAVISPDRRTHGLLIQKDGGYESQPVDVVLPMIHG KFGEDGTIQGLLELSGIPYVGCDIQSSVTCMDKSLAYMVVKNAGIEVPGF RVLQKGDSLKAETLSYPVFVKPARSGSSFGVNKVCRAEELQAAVTEAGKY DCKILVEEAVSGSEVGCAILGNENALMAGEVDQIELRHGFFKIHQEAQPE KGSENAVIRVPAVLPDEVRERIQKTAMKIYRILGCRGLARIDLFLREDGC IVLNEVNTMPGFTSYSRYPRMMTAAGFTLTEILDRLIELSLRR SEQ ID No. 79: MYRINVAVLFGGCSEEHTVSIKSAMELAANIDTEKYQPFYIGITKSGVWK LCEKPCLDWEQYAKYPVVFSPGRNTHGFLIQKEDRYEIQPVDVVFPIIHG KFGEDGSIQGLLELSGIPYVGCDIQSSVICMDKSLAYTTVKNAGIEVPDF QIIQDGDSPKTECFSFPLFVKPARSGSSFGVNKVDKAEDLCAAINEARQY DRKVLIEQAVSGSEVGCAVLGTGTDLIVGEVDQISLKHGFFKIHQEAQPE KGSENATIEVPADLPAKVRERIQKTAKKIYQVLGCRGLARIDLFLREDGH IVLNEVNTMPGFTSYSRYPCMMTAAGFTLSELIDRLIELALRR said peptides of type VanD preferably being selected from the peptides of sequence SEQ ID No. 80 to SEQ ID No. 83 as defined below:

Peptide Amino acid Position of the peptide in the VanD SEQ ID No. sequence protein or proteins SEQ ID No. GSENAVIR 252-259 for the proteins of SEQ No. 72, 80 73, 74, 75, 76, 77, 78 SEQ ID No. IDLFLR 291-296 for the proteins of SEQ No. 72, 81 73, 74, 75, 76, 77, 78, 79 SEQ ID No. IHQEAQPEK 243-251 for the proteins of SEQ No. 72, 82 73, 74, 75, 76, 77, 78, 79 SEQ ID No. SGSSFGVNK 175-183 for the proteins of SEQ No. 72, 83 73, 74, 75, 76, 77, 78, 79

Advantageously, the markers of type VanD selected from the peptides of sequence SEQ ID No. 80, SEQ ID No. 81 and SEQ ID No. 83 are detected after induction of the mechanism of resistance.

Advantageously, the markers of type VanD selected from the peptides of sequence SEQ ID No. 80, SEQ ID No. 81 and SEQ ID No. 83 are detected without an induction step.

According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, induced by expression of the protein VanE, is characterized by the detection of at least one peptide belonging to the protein VanE of sequence SEQ ID No. 84.

SEQ ID No. 84: MKTVAIIFGGVSSEYEVSLKSAVAIIKNMESIDYNVMKIGITEEGHWYLF EGTTDKIKKDRWFLDESCEEIVVDFAKKSFVLKNSKKIIKPDILFPVLHG GYGENGAMQGVFELLDIPYVGCGIGAAAISMNKIMLHQFAEAIGVKSTPS MIIEKGQDLQKVDAFAKIHGFPLYIKPNEAGSSKGISKVERKSDLYKAID EASKYDSRILIQKEVKGVEIGCGILGNEQLVVGECDQISLVDGFFDYEEK YNLVTAEILLPAKLSIDKKEDIQMKAKKLYRLLGCKGLARIDFFLTDDGE ILLNEINTMPGFTEHSRFPMMMNEIGMDYKEIIENLLVLAVENHEKKLST ID said markers of type VanE preferably being selected from the peptides of sequence SEQ ID No. 85 to SEQ ID No. 91 as defined below:

Peptide Amino acid Position of the peptide in the VanE SEQ ID No. sequence protein or proteins SEQ ID No. AIDEASK 198-204 for the protein of SEQ No. 84 85 SEQ ID No. FPMMMNEIGMDYK 318-330 for the protein of SEQ No. 84 86 SEQ ID No. IMLHQFAEAIGVK 134-146 for the protein of SEQ No. 84 87 SEQ ID No. NMESIDYNVMK 28-38 for the protein of SEQ No. 84 88 SEQ ID No. SAVAIIK 21-27 for the protein of SEQ No. 84 89 SEQ ID No. STPSMIIEK 147-155 for the protein of SEQ No. 84 90 SEQ ID No. YNLVTAEILLPAK 251-263 for the protein of SEQ No. 84 91

Advantageously, the marker of type VanE corresponding to the peptide of sequence SEQ ID No. 89 is detected after induction of the mechanism of resistance.

According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanG, is characterized by the detection of at least one peptide belonging to the protein VanG and its different variants of sequences SEQ ID No. 92 to SEQ ID No. 94.

SEQ ID No. 92: MIKKRIAIIFGGNSTEYEVSLQSASAVFENINTKKFDIVPIGITRNGDWY HYTGKKEKIANNTWFEDNENLYSVAVSQNRSVKGFIEFKEEKFYIIKVDL IFPVLHGKNGEDGTLQGLFELAGIPVVGCDTLSSALCMDKDKAHKLVSLA GISVPKSVTFKFSGKKAALKKIEKELSYPLFVKPVRAGSSFGITKVTKQQ ELENAIQLAFEHDAEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSG FFDYTEKYTLKSSKIYMPARIDAEAEKRIQETAVTIYKALGCSGFSRVDM FYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFAQMLDKLIGLYVE SEQ ID No. 93: MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWY HYTGEKEKILNNTWFEDSKNLCPVVVSQNRSVKGFLEIASDKYRIIKVDL VFPVLHGKNGEDGTLQGIFELAGIPVVGCDTLSSALCMDKDRAHKLVSLA GISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQ ELDAAIELAFEHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSG FFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYKALGCSGFSRVDM FYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYVE SEQ ID No. 94: MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWY HYTGEKEKILNNTWFEDSKNLCPVVVSQNRSVKGFLEIASDKYRIIKVDL VFPVLHGKNGENGTLQGIFELAGIPVVGCDTLSSALCMDKDRAHKLVSLA GISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQ ELDAAIELAFEHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSG FFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYKALGCSGFSRVDM FYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYVE said markers of type VanG preferably being selected from the peptides of sequence SEQ ID No. 95 to SEQ ID No. 102 as defined below:

Peptide SEQ ID Amino acid Position of the peptide in the No. sequence VanG protein or proteins SEQ ID AGSSFGITK 187-195 for the proteins of SEQ No. 95 No. 92, 93, 94 SEQ ID ALGCSGFSR 289-297 for the proteins of SEQ No. 96 No. 92, 93, 94 SEQ ID IDAEAEK 271-277 for the proteins of SEQ No. 97 No. 92, 93, 94 SEQ ID IYMPAR 265-270 for the proteins of SEQ No. 98 No. 92, 93, 94 SEQ ID LIGLYVE 343-349 for the proteins of SEQ No. 99 No. 92, 93, 94 SEQ ID LVSLAGISVPK 146-156 for the proteins of SEQ No. 100 No. 92, 93, 94 SEQ ID VDEIELSSGFFDYTEK 242-257 for the proteins of SEQ No. 101 No. 92, 93, 94 SEQ ID YPNMMK 325-330 for the proteins of SEQ No. 102 No. 92, 93, 94

Advantageously, the markers of type VanG selected from the peptides of sequence SEQ ID No. 95, SEQ ID No. 96, SEQ ID No. 97, SEQ ID No. 98, SEQ ID No. 100 and SEQ ID No. 102 are detected after induction of the mechanism of resistance.

Advantageously, the markers of type VanG selected from the peptides of sequence SEQ ID No. 97 and SEQ ID No. 100 are detected without an induction step.

According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, induced by expression of the protein VanL, is characterized by the detection of at least one peptide belonging to the protein VanL of sequence SEQ ID No. 103.

SEQ ID No. 103: MMKLKKIAIIFGGQSSEYEVSLKSTVSVLETLSTCNFEIIKIGIDLGGKW YLTTSNNKDIEYDVWQTDPSLQEIIPCFNNRGFYNKTTNKYFRPDVLFPI LHGGTGEDGTLQGVFELMNIPYVGCGVTPSAICMDKYLLHEFAQSVGVKS APTLIIRTRNCKDEIDKFIEKNDFPIFVKPNEAGSSKGINKVNEPDKLED ALTEAFKYSKSVIIQKAIIGREIGCAVLGNEKLLVGECDEVSLNSDFFDY TEKYQMISAKVNIPASISVEFSNEMKKQAQLLYRLLGCSGLARIDFFLSD NNEILLNEINTLPGFTEHSRYPKMMEAVGVTYKEIITKLINLAEEKYYG said peptides of type VanL preferably being selected from the peptides of sequence SEQ ID No. 104 to SEQ ID No. 120 as defined below:

Peptide SEQ ID Position of the peptide in the VanL No. Amino acid sequence protein or proteins SEQ ID DIEYDVWQTDPSLQEIIPCFNNR 59-81 for the protein of SEQ No. 103 No. 104 SEQ ID EIGCAVLGNEK 222-232 for the protein of SEQ No. No. 105 103 SEQ ID IAIIFGGQSSEYEVSLK 7-23 for the protein of SEQ No. 103 No. 106 SEQ ID IGIDLGGK 42-49 for the protein of SEQ No. 103 No. 107 SEQ ID LEDALTEAFK 198-207 for the protein of SEQ No. No. 108 103 SEQ ID LINLAEEK 339-346 for the protein of SEQ No. No. 109 103 SEQ ID LLGCSGLAR 285-293 for the protein of SEQ No. No. 110 103 SEQ ID LLVGECDEVSLNSDFFDYTEK 233-253 for the protein of SEQ No. No. 111 103 SEQ ID MMEAVGVTYK 324-333 for the protein of SEQ No. No. 112 103 SEQ ID NDFPIFVKPNEAGSSK 172-187 for the protein of SEQ No. No. 113 103 SEQ ID QAQLLYR 278-284 for the protein of SEQ No. No. 114 103 SEQ ID SAPTLIIR 150-157 for the protein of SEQ No. No. 115 103 SEQ ID STVSVLETLSTCNFEIIK 24-41 for the protein of SEQ No. 103 No. 116 SEQ ID VNIPASISVEFSNEMK 261-276 for the protein of SEQ No. No. 117 103 SEQ ID WYLTTSNNK 50-58 for the protein of SEQ No. 103 No. 118 SEQ ID YLLHEFAQSVGVK 137-149 for the protein of SEQ No. No. 119 103 SEQ ID YQMISAK 254-260 for the protein of SEQ No. No. 120 103

According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, induced by expression of the protein VanM, is characterized by the detection of at least one peptide belonging to the protein VanM of sequence SEQ ID No. 121.

SEQ ID No. 121: MNRLKIAILFGGCSEEHNVSVKSAAEIANNIDIGKYEPIYIGITQSGVWK TCEKPCIDWDNEHCRSAVLSPDKKMHGLLIMQDKGYQIQRIDVVFSVLHG KSGEDGAIQGLFELSGIPYVGCDIQSSAVCMDKSLAYIIAKNAGIATPEF QVIYKDDKPAADSFTYPVFVKPARSGSSYGVNKVNSADELDSAIDLARQY DSKILIEQGVLGYEVGCAVLGNSFDLIVGEVDQIRLQHGIFRIHQEAEPE KGSENATITVPAELSAEERERIKEAAKNIYKALGCRGLSRVDMFLQDNGR IVLNEVNTMPGFTSYSRYPRMMVSAGITIPELIDHLIVLAVKE said peptides of type VanM preferably being selected from the peptides of sequence SEQ ID No. 122 to SEQ ID No. 139 as defined below:

Peptide SEQ ID Position of the peptide in the No. Amino acid sequence VanM protein or proteins SEQ ID DDKPAADSFTYPVFVKPAR 156-174 for the protein of SEQ No. 122 No. 121 SEQ ID GSENATITVPAELSAEER 252-269 for the protein of SEQ No. 123 No. 121 SEQ ID IAILFGGCSEEHNVSVK 6-22 for the protein of SEQ No. No. 124 121 SEQ ID IDVVFSVLHGK 91-101 for the protein of SEQ No. 125 No. 121 SEQ ID IHQEAEPEK 243-251 for the protein of SEQ No. 126 No. 121 SEQ ID IVLNEVNTMPGFTSYSR 301-317 for the protein of SEQ No. 127 No. 121 SEQ ID LQHGIFR 236-242 for the protein of SEQ No. 128 No. 121 SEQ ID MHGLLIMQDK 75-84 for the protein of SEQ No. No. 129 121 SEQ ID MMVSAGITIPELIDHLIVLAVK 321-342 for the protein of SEQ No. 130 No. 121 SEQ ID NAGIATPEFQVIYK 142-155 for the protein of SEQ No. 131 No. 121 SEQ ID SAAEIANNIDIGK 23-35 for the protein of SEQ No. No. 132 121 SEQ ID SAVLSPDK 66-73 for the protein of SEQ No. No. 133 121 SEQ ID SGSSYGVNK 175-183 for the protein of SEQ No. 134 No. 121 SEQ ID SLAYIIAK 134-141 for the protein of SEQ No. 135 No. 121 SEQ ID TCEKPCIDWDNEHCR 51-65 for the protein of SEQ No. No. 136 121 SEQ ID VDMFLQDNGR 291-300 for the protein of SEQ No. 137 No. 121 SEQ ID VNSADELDSAIDLAR 184-198 for the protein of SEQ No. 138 No. 121 SEQ ID YEPIYIGITQSGVWK 36-50 for the protein of SEQ No. No. 139 121

According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, induced by expression of the protein VanN, is characterized by the detection of at least one peptide belonging to the protein VanN of sequence SEQ ID No. 140.

SEQ ID No. 140: MKKIALIFGGTSAEYEVSLKSAASVLSVLENLNVEIYRIGIASNGKWYLT FSDNETIANDLWLQDKKLNEITPSFDGRGFYDQAEKVYFKPDVLFPMLHG GTGENGTLQGVFECMQIPYVGCGVASSAICMNKYLLHQFAKSVGVMSTPT QLISSTDEQQVIKNFTELYGFPIFIKPNEAGSSKGISKVHTEAELTKALT EAFQFSQTVILQKAVSGVEIGCAILGNDQLLVGECDEVSLATDFFDYTEK YQMTTAKLTVPAKIPVATSREIKRQAQLLYQLLGCQGLARIDFFLTEAGE ILLNEINTMPGFTNHSRFPAMMAATGITYQELISTLITLAEDK said peptides of type VanN preferably being selected from the peptides of sequence SEQ ID No. 141 to SEQ ID No. 154 as defined below:

Peptide SEQ ID Position of the peptide in the No. Amino acid sequence protein VanN SEQ ID ALTEAFQFSQTVILQK 198-213 for the protein of SEQ No. 141 No. 140 SEQ ID GFYDQAEK 79-86 for the protein of SEQ No. No. 142 140 SEQ ID IALIFGGTSAEYEVSLK 4-20 for the protein of SEQ No. No. 143 140 SEQ ID IGIASNGK 39-46 for the protein of SEQ No. No. 144 140 SEQ ID IPVATSR 264-270 for the protein of SEQ No. 145 No. 140 SEQ ID LNEITPSFDGR 68-78 for the protein of SEQ No. No. 146 140 SEQ ID NFTELYGFPIFIKPNEAGSSK 164-184 for the protein of SEQ No. 147 No. 140 SEQ ID QAQLLYQLLGCQGLAR 275-290 for the protein of SEQ No. 148 No. 140 SEQ ID SAASVLSVLENLNVEIYR 21-38 for the protein of SEQ No. No. 149 140 SEQ ID SVGVMSTPTQLISSTDEQQVIK 142-163 for the protein of SEQ No. 150 No. 140 SEQ ID VHTEAELTK 189-197 for the protein of SEQ No. 151 No. 140 SEQ ID WYLTFSDNETIANDLWLQDK 47-66 for the protein of SEQ No. No. 152 140 SEQ ID YLLHQFAK 134-141 for the protein of SEQ No. 153 No. 140 SEQ ID YQMTTAK 251-257 for the protein of SEQ No. 154 No. 140

The method of the invention and its advantages will become clearer from the rest of the present description, which presents several nonlimiting embodiment examples of said method.

EXAMPLE 1 Preparation of a Primary Urine Sample by Enrichment with Microorganisms

The following protocol is carried out in 16 steps (steps 5 to 12 are optional and could be omitted if the enriched sample is treated subsequently according to example 6 and the subsequent examples):

-   -   1. Centrifugation of 5 mL of contaminated urine, at 2000 g for         30 seconds     -   2. Recovery of the supernatant     -   3. Centrifugation at 15000 g for 5 minutes     -   4. Removal of the supernatant     -   5. Washing of the pellet with 3 mL of distilled water by         resuspension     -   6. Centrifugation at 15000 g for 5 minutes     -   7. Removal of the supernatant     -   8. Put the pellet in contact with solvent (8 volumes acetone to         1 volume of methanol) at 1/10 dilution     -   9. Leave for 1 hour at −20° C.     -   10. Centrifugation at 15000 g for 5 minutes     -   11. Removal of the supernatant     -   12. Put the pellet in contact with solvent (8 volumes acetone to         1 volume of methanol) at 1/10 dilution     -   13. Leave for 1 hour at −20° C.     -   14. Centrifugation at 15000 g for 5 minutes     -   15. Removal of the supernatant         The pellet constitutes the sample enriched with microorganism.

EXAMPLE 2 Culture of the Sample on Culture Medium in the Absence of Antibiotic

The optimal culture media and the optimal culture conditions are different depending on the species of microorganism. By default, the sample is seeded on various media:

-   -   Columbia sheep blood agar (bioMérieux reference 43041) for 18 to         24 h at 35° C., in aerobic or anaerobic atmosphere;     -   TSA agar (bioMérieux reference 43011) for 18 to 24 h at 37° C.

EXAMPLE 3 Culture of the Sample on Culture Medium in the Presence of Antibiotic

The sample is seeded on medium:

-   -   VRE agar (bioMérieux reference 43002) for 18 to 24 h at 35° C.,         in aerobic or anaerobic atmosphere. This medium contains         vancomycin.

EXAMPLE 4 Identification of Microorganisms by Biochemical Profile

Identification is performed as follows:

-   -   1. Selection of isolated colonies obtained according to example         2 or example 3, or by enrichment of microorganisms present in a         primary sample according to example 1.     -   2. Observing aseptic conditions, transfer of 3.0 mL of sterile         aqueous saline solution (at 0.45-0.50% of NaCl, of pH 4.5 to         7.0) to a transparent plastic (polystyrene) test tube     -   3. Using a rod or a sterile swab, transfer of a sufficient         number of identical colonies to the tube of saline solution         prepared in step 2 and adjustment of the bacterial suspension         between 0.50 and 0.63 McFarland with a calibrated DENSICHEK of         the VITEK®     -   4. Placement of the tube of bacterial suspension and of a VITEK®         identification card on a VITEK® cassette     -   5. Loading of the cassette in the VITEK® instrument     -   6. The operations of filling, sealing, incubation and reading         are automatic     -   7. Acquisition of a biochemical profile         Identification with the VITEK® system carried out by comparison         with biochemical profiles of known strains

EXAMPLE 5 Identification of Microorganisms from a Sample by MALDI-TOF

Identification is performed as follows:

-   -   1. Transfer, using a 1 μl loop, of a portion of microorganism         colony obtained according to example 2 or 3, or of an enriched         sample according to example 1, and uniform deposition on a plate         for mass spectrometry by MALDI-TOF     -   2. Covering the deposit with 1 μl of matrix. The matrix used is         a saturated solution of HCCA (alpha-cyano-4-hydroxycinnamic         acid) in organic solvent (50% acetonitrile and 2.5%         trifluoroacetic acid)     -   3. Drying at room temperature     -   4. Putting the plate in the mass spectrometer     -   5. Acquisition of a mass spectrum     -   6. Comparison of the spectrum obtained with the spectra         contained in a knowledge base     -   7. Identification of the microorganism by comparing the peaks         obtained with those in the knowledge base

EXAMPLE 6 Identification of Microorganisms from a Sample by ESI-MS

Identification is performed as follows:

-   -   1. Sampling of a microorganism colony obtained according to         example 2 or 3, or of an enriched sample according to example 1,         and suspension in 100 μl of demineralized water.     -   2. Centrifugation at 3000 g for 5 minutes.     -   3. Removal of the supernatant.     -   4. Resuspension in 100 μl of demineralized water.     -   5. Centrifugation at 3000 g for 5 minutes.     -   6. Removal of the supernatant.     -   7. Resuspension in 100 μl of a mixture of acetonitrile,         demineralized water, formic acid (50/50/0.1%).     -   8. Filtration with a filter of porosity 0.45 μm.     -   9. Injection in a mass spectrometer in single MS mode.     -   10. Acquisition of a mass spectrum.     -   11. Comparison of the spectrum obtained with the spectra         contained in a knowledge base.     -   12. Identification of the microorganism by reference to         reference spectra.

EXAMPLE 7 Obtaining Digested Proteins from Microorganisms

The following protocol is carried out in 17 steps:

-   -   1. Sampling a microorganism colony, obtained according to         example 2 or 3, or an enriched sample according to example 1,         and suspension in 10 to 100 μl of a 6M solution of guanidine         hydrochloride, 50 mM Tris-HCl, pH=8.0.     -   2. Addition of dithiothreitol (DTT) to obtain a final         concentration of 5 mM.     -   3. Reduction for 20 minutes at 95° C. in a water bath.     -   4. Cooling of the tubes to room temperature.     -   5. Addition of iodoacetamide to obtain a final concentration of         12.5 mM.     -   6. Alkylation for 40 minutes at room temperature in the dark.     -   7. Dilution by a factor of 6 with a 50 mM solution of NH₄HCO₃,         pH=8.0 to obtain a final concentration of guanidine         hydrochloride of 1M.     -   8. Addition of 1 μg of trypsin.     -   9. Digestion at 37° C. for 6 hours overnight.     -   10. Addition of formic acid until the pH is below 4 to stop the         reaction.     -   11. The sample volume is made up to 1 mL with water/formic acid         0.5% (v/v).     -   12. Equilibration of the Waters Oasis HLB columns with 1 ml of         methanol and then 1 ml H₂O/formic acid 0.1% (v/v)     -   13. Deposition of the sample, which flows by gravity     -   14. Washing with 1 ml H₂O/formic acid 0.1% (v/v)     -   15. Elution with 1 ml of a mixture of 80% of methanol and 20% of         water/formic acid 0.1% (v/v)     -   16. The eluate is evaporated with an evaporator of the SpeedVac®         SPD2010 type (Thermo Electron Corporation, Waltham, Mass.,         United States of America), for 2 hours, to obtain a volume of         about 100 μl.         The eluate is then taken up in a solution of water/formic acid         0.5% (v/v) quantity sufficient (Q.S.) for 200 μl

EXAMPLE 8 Identification of Resistance to Glycopeptides, without Induction, of Type VanA, VanB, VanC1, VanD, VanE and VanG

Samples Smp1 to Smp13 are identified according to one of the methods described in examples 1 to 6. Identification of the species is reported in TABLE 1.

TABLE 1 Name Species Smp1 E. faecalis Smp2 E. gallinarum Smp3 E. faecalis Smp4 E. faecalis Smp5 E. faecalis Smp6 E. faecalis Smp7 E. faecalis Smp8 E. faecium Smp9 E. faecium Smp10 E. faecalis Smp11 E. faecium Samples Smp1 to Smp11 correspond to a species that may comprise a mechanism of resistance of the Van type. The following method is then employed for investigating such a mechanism.

The microorganism colony is obtained according to example 2, treated according to example 7, and then a volume of 50 μl of digested proteins is injected and analyzed according to the following conditions:

-   -   Dionex Ultimate 3000 chromatographic chain from the company         Dionex Corporation (Sunnyvale, United States of America).     -   Waters BEH130 C18 column, 2.1 mm inside diameter, length 100 mm,         particle size 3.5 μm (Waters, Saint-Quentin en Yvelines,         France).     -   Solvent A: H₂O+0.1% formic acid.     -   Solvent B: ACN+0.1% formic acid.         HPLC gradient defined in TABLE 2 below.

TABLE 2 Time (min) Flow (μl) Solvent A (%) Solvent B (%) 0 300 98 2 3 300 98 2 28 300 63 37 30 300 0 100 38 300 0 100 38.1 300 98 2 45 300 98 2

-   -   The eluate leaving the chromatographic column is directly         injected in the ionization source of the mass spectrometer of         the QTRAP® 5500 type from the company Applied Biosystems (Foster         City, United States of America).     -   The peptides resulting from digestion of the proteins of the         microorganism are analyzed by the mass spectrometer in MRM mode.         Only the peptides shown in TABLE 3 are detected. For this, the         fragment or fragments shown in TABLE 3 are detected.

TABLE 3 State of Transition charge of First-generation number Protein Peptide precursor ion fragment   1 VanA IHQEVEPEK 2 y5 single-charged (SEQ ID No. 5)   2 VanA IHQEVEPEK 2 y6 single-charged (SEQ ID No. 5)   3 VanA IHQEVEPEK 2 y7 single-charged (SEQ ID No. 5)   4 VanA LIVLALK 2 y4 single-charged (SEQ ID No. 6)   5 VanA LIVLALK 2 y5 single-charged (SEQ ID No. 6)   6 VanA LIVLALK 2 y6 single-charged (SEQ ID No. 6)   7 VanA LQYGIFR 2 y4 single-charged (SEQ ID No. 7)   8 VanA LQYGIFR 2 y5 single-charged (SEQ ID No. 7)   9 VanA LQYGIFR 2 y6 single-charged (SEQ ID No. 7)  10 VanA MHGLLVK 2 b5 single-charged (SEQ ID No. 8)  11 VanA MHGLLVK 2 y5 single-charged (SEQ ID No. 8)  12 VanA MHGLLVK 2 y6 single-charged (SEQ ID No. 8)  13 VanA MMAAAGIALPELIDR 2 y6 single-charged (SEQ ID No. 9)  14 VanA MMAAAGIALPELIDR 2 y7 single-charged (SEQ ID No. 9)  15 VanA MMAAAGIALPELIDR 2 y8 single-charged (SEQ ID No. 9)  16 VanA NAGIATPAFWVINK 2 y10 single-charged (SEQ ID No. 10)  17 VanA NAGIATPAFWVINK 2 y8 single-charged (SEQ ID No. 10)  18 VanA NAGIATPAFWVINK 2 y9 single-charged (SEQ ID No. 10)  19 VanA SAIEIAANINK 2 y6 single-charged (SEQ ID No. 11)  20 VanA SAIEIAANINK 2 y7 single-charged (SEQ ID No. 11)  21 VanA SAIEIAANINK 2 y8 single-charged (SEQ ID No. 11)  22 VanA SGSSFGVK 2 y5 single-charged (SEQ ID No. 12)  23 VanA SGSSFGVK 2 y6 single-charged (SEQ ID No. 12)  24 VanA SGSSFGVK 2 y7 single-charged (SEQ ID No. 12)  25 VanA SLTYIVAK 2 y4 single-charged (SEQ ID No. 13)  26 VanA SLTYIVAK 2 y5 single-charged (SEQ ID No. 13)  27 VanA SLTYIVAK 2 y6 single-charged (SEQ ID No. 13)  28 VanA VDMFLQDNGR 2 y6 single-charged (SEQ ID No. 14)  29 VanA VDMFLQDNGR 2 y7 single-charged (SEQ ID No. 14)  30 VanA VDMFLQDNGR 2 y8 single-charged (SEQ ID No. 14)  31 VanA VNSADELDYAIESAR 2 y6 single-charged (SEQ ID No. 15)  32 VanA VNSADELDYAIESAR 2 y7 single-charged (SEQ ID No. 15)  33 VanA VNSADELDYAIESAR 2 y8 single-charged (SEQ ID No. 15)  34 VanA YEPLYIGITK 2 y7 single-charged (SEQ ID No. 16)  35 VanA YEPLYIGITK 2 y8 single-charged (SEQ ID No. 16)  36 VanA YEPLYIGITK 2 y8 double-charged (SEQ ID No. 16)  37 VanB FDPHYIGITK 2 y6 single-charged (SEQ ID No. 29)  38 VanB FDPHYIGITK 2 y7 double-charged (SEQ ID No. 29)  39 VanB FDPHYIGITK 2 y8 double-charged (SEQ ID No. 29)  40 VanB IDVAFPVLHGK 2 y6 single-charged (SEQ ID No. 30)  41 VanB IDVAFPVLHGK 2 y7 single-charged (SEQ ID No. 30)  42 VanB IDVAFPVLHGK 2 y8 single-charged (SEQ ID No. 30)  43 VanB IHQENEPEK 2 y5 single-charged (SEQ ID No. 31)  44 VanB IHQENEPEK 2 y6 single-charged (SEQ ID No. 31)  45 VanB IHQENEPEK 2 y7 single-charged (SEQ ID No. 31)  46 VanB LSHGIFR 2 y4 single-charged (SEQ ID No. 32)  47 VanB LSHGIFR 2 y5 single-charged (SEQ ID No. 32)  48 VanB LSHGIFR 2 y6 single-charged (SEQ ID No. 32)  49 VanB SLAYILTK 2 y5 single-charged (SEQ ID No. 33)  50 VanB SLAYILTK 2 y6 single-charged (SEQ ID No. 33)  51 VanB SLAYILTK 2 y7 single-charged (SEQ ID No. 33)  52 VanB THGLLVMK 2 b5 single-charged (SEQ ID No. 34)  53 VanB THGLLVMK 2 b6 single-charged (SEQ ID No. 34)  54 VanB THGLLVMK 2 y6 single-charged (SEQ ID No. 34)  55 VanB VQETAK 2 y3 single-charged (SEQ ID No. 35)  56 VanB VQETAK 2 y4 single-charged (SEQ ID No. 35)  57 VanB VQETAK 2 y5 single-charged (SEQ ID No. 35)  58 VanC1 EQAQLLYR 2 y3 single-charged (SEQ ID No. 59)  59 VanC1 EQAQLLYR 2 y4 single-charged (SEQ ID No. 59)  60 VanC1 EQAQLLYR 2 y6 single-charged (SEQ ID No. 59)  61 VanC1 FIQDHGFPIFIKPNEAGSSK 3 b7 single-charged (SEQ ID No. 60)  62 VanC1 FIQDHGFPIFIKPNEAGSSK 3 y8 single-charged (SEQ ID No. 60)  63 VanC1 FIQDHGFPIFIKPNEAGSSK 3 y9 single-charged (SEQ ID No. 60)  64 VanC1 IVPDVLFPVLHGK 2 y11 double- (SEQ ID No. 61) charged  65 VanC1 IVPDVLFPVLHGK 3 y11 double- (SEQ ID No. 61) charged  66 VanC1 IVPDVLFPVLHGK 3 y11 triple-charged (SEQ ID No. 61)  67 VanC1 NC[CAM]HQLTFSSQGFILGEK 3 y5 single-charged (SEQ ID No. 62)  68 VanC1 NC[CAM]HQLTFSSQGFILGEK 3 y7 single-charged (SEQ ID No. 62)  69 VanC1 NC[CAM]HQLTFSSQGFILGEK 3 y8 single-charged (SEQ ID No. 62)  70 VanC1 NDTWLEDHK 2 y5 single-charged (SEQ ID No. 63)  71 VanC1 NDTWLEDHK 2 y6 single-charged (SEQ ID No. 63)  72 VanC1 NDTWLEDHK 2 y7 single-charged (SEQ ID No. 63)  73 VanC1 NLGLTGLAR 2 y4 single-charged (SEQ ID No. 64)  74 VanC1 NLGLTGLAR 2 y5 single-charged (SEQ ID No. 64)  75 VanC1 NLGLTGLAR 2 y7 single-charged (SEQ ID No. 64)  76 VanC1 TALQSALTTAFAYGSTVLIQK 3 y7 single-charged (SEQ ID No. 65)  77 VanC1 TALQSALTTAFAYGSTVLIQK 3 y8 single-charged (SEQ ID No. 65)  78 VanC1 TALQSALTTAFAYGSTVLIQK 3 y9 single-charged (SEQ ID No. 65)  79 VanC1 WLLHQLADTMGIASAPTLLLSR 3 y10 single-charged (SEQ ID No. 66)  80 VanC1 WLLHQLADTMGIASAPTLLLSR 3 y7 single-charged (SEQ ID No. 66)  81 VanC1 WLLHQLADTMGIASAPTLLLSR 3 y9 single-charged (SEQ ID No. 66)  82 VanC1 YENDPATIDR 2 b4 single-charged (SEQ ID No. 67)  83 VanC1 YENDPATIDR 2 y6 single-charged (SEQ ID No. 67)  84 VanC1 YENDPATIDR 2 y8 single-charged (SEQ ID No. 67)  85 VanC1 YQLISATITVPAPLPLALESQIK 3 y11 double- (SEQ ID No. 68) charged  86 VanC1 YQLISATITVPAPLPLALESQIK 3 y13 double- (SEQ ID No. 68) charged  87 VanC1 YQLISATITVPAPLPLALESQIK 3 y9 single-charged (SEQ ID No. 68)  88 VanC2 ITVPAPLPETIETK 2 y11 double- (SEQ ID No. 69) charged  89 VanC2 ITVPAPLPETIETK 2 y7 single-charged (SEQ ID No. 69)  90 VanC2 ITVPAPLPETIETK 2 y9 single-charged (SEQ ID No. 69)  91 VanC2 QDTWLLDTK 2 y4 single-charged (SEQ ID No. 70)  92 VanC2 QDTWLLDTK 2 y5 single-charged (SEQ ID No. 70)  93 VanC2 QDTWLLDTK 2 y6 single-charged (SEQ ID No. 70)  94 VanC2 YQLISAK 2 y3 single-charged (SEQ ID No. 71)  95 VanC2 YQLISAK 2 y5 single-charged (SEQ ID No. 71)  96 VanC2 YQLISAK 2 y6 single-charged (SEQ ID No. 71)  97 VanD GSENAVIR 2 y4 single-charged (SEQ ID No. 80)  98 VanD GSENAVIR 2 y5 single-charged (SEQ ID No. 80)  99 VanD GSENAVIR 2 y6 single-charged (SEQ ID No. 80) 100 VanD IDLFLR 2 y3 single-charged (SEQ ID No. 81) 101 VanD IDLFLR 2 y4 single-charged (SEQ ID No. 81) 102 VanD IDLFLR 2 y5 single-charged (SEQ ID No. 81) 103 VanD IHQEAQPEK 2 y3 single-charged (SEQ ID No. 82) 104 VanD IHQEAQPEK 2 y7 single-charged (SEQ ID No. 82) 105 VanD IHQEAQPEK 2 y8 double-charged (SEQ ID No. 82) 106 VanD SGSSFGVNK 2 y5 single-charged (SEQ ID No. 83) 107 VanD SGSSFGVNK 2 y6 single-charged (SEQ ID No. 83) 108 VanD SGSSFGVNK 2 y7 single-charged (SEQ ID No. 83) 109 VanE AIDEASK 2 y4 single-charged (SEQ ID No. 85) 110 VanE AIDEASK 2 y5 single-charged (SEQ ID No. 85) 111 VanE AIDEASK 2 y6 single-charged (SEQ ID No. 85) 112 VanE FPMMMNEIGMDYK 2 y9 single-charged (SEQ ID No. 86) 113 VanE FPMMMNEIGMDYK 2 y12 double- (SEQ ID No. 86) charged 114 VanE FPMMMNEIGMDYK 2 y5 single-charged (SEQ ID No. 86) 115 VanE IMLHQFAEAIGVK 2 y10 double- (SEQ ID No. 87) charged 116 VanE IMLHQFAEAIGVK 2 y8 single-charged (SEQ ID No. 87) 117 VanE IMLHQFAEAIGVK 2 y9 single-charged (SEQ ID No. 87) 118 VanE NMESIDYNVMK 2 y6 single-charged (SEQ ID No. 88) 119 VanE NMESIDYNVMK 2 y7 single-charged (SEQ ID No. 88) 120 VanE NMESIDYNVMK 2 y8 single-charged (SEQ ID No. 88) 121 VanE SAVAIIK 2 y4 single-charged (SEQ ID No. 89) 122 VanE SAVAIIK 2 y5 single-charged (SEQ ID No. 89) 123 VanE SAVAIIK 2 y6 single-charged (SEQ ID No. 89) 124 VanE STPSMIIEK 2 y6 single-charged (SEQ ID No. 90) 125 VanE STPSMIIEK 2 y7 single-charged (SEQ ID No. 90) 126 VanE STPSMIIEK 2 y7 double-charged (SEQ ID No. 90) 127 VanE YNLVTAEILLPAK 2 y4 single-charged (SEQ ID No. 91) 128 VanE YNLVTAEILLPAK 2 y8 single-charged (SEQ ID No. 91) 129 VanE YNLVTAEILLPAK 2 y9 single-charged (SEQ ID No. 91) 130 VanG AGSSFGITK 2 y5 single-charged (SEQ ID No. 95) 131 VanG AGSSFGITK 2 y7 single-charged (SEQ ID No. 95) 132 VanG AGSSFGITK 2 y8 single-charged (SEQ ID No. 95) 133 VanG ALGC[CAM]SGFSR 2 y5 single-charged (SEQ ID No. 96) 134 VanG ALGC[CAM]SGFSR 2 y6 single-charged (SEQ ID No. 96) 135 VanG ALGC[CAM]SGFSR 2 y7 single-charged (SEQ ID No. 96) 136 VanG IDAEAEK 2 y4 single-charged (SEQ ID No. 97) 137 VanG IDAEAEK 2 y5 single-charged (SEQ ID No. 97) 138 VanG IDAEAEK 2 y6 single-charged (SEQ ID No. 97) 139 VanG IYMPAR 2 y3 single-charged (SEQ ID No. 98) 140 VanG IYMPAR 2 y4 single-charged (SEQ ID No. 98) 141 VanG IYMPAR 2 y5 single-charged (SEQ ID No. 98) 142 VanG LIGLYVE 2 b4 single-charged (SEQ ID No. 99) 143 VanG LIGLYVE 2 b5 single-charged (SEQ ID No. 99) 144 VanG LIGLYVE 2 b6 single-charged (SEQ ID No. 99) 145 VanG LVSLAGISVPK 2 y6 single-charged (SEQ ID No. 100) 146 VanG LVSLAGISVPK 2 y7 single-charged (SEQ ID No. 100) 147 VanG LVSLAGISVPK 2 y9 single-charged (SEQ ID No. 100) 148 VanG VDEIELSSGFFDYTEK 2 y10 single-charged (SEQ ID No. 101) 149 VanG VDEIELSSGFFDYTEK 2 y4 single-charged (SEQ ID No. 101) 150 VanG VDEIELSSGFFDYTEK 2 y6 single-charged (SEQ ID No. 101) 151 VanG YPNMMK 2 y3 single-charged (SEQ ID No. 102) 152 VanG YPNMMK 2 y4 single-charged (SEQ ID No. 102) 153 VanG YPNMMK 2 y5 single-charged (SEQ ID No. 102)

The transitions mentioned in TABLE 3 are detected using the parameters shown in TABLES 4 and 5.

TABLE 4 (m/z) (m/z) Collision Transition Retention filtered in filtered in energy number time Q1 Q3 (eV) 1 8.75 554.79 601.32 29 2 8.75 554.79 730.36 29 3 8.75 554.79 858.42 29 4 19.71 385.28 444.32 22 5 19.71 385.28 543.39 22 6 19.71 385.28 656.47 22 7 17.91 448.75 492.29 25 8 17.91 448.75 655.36 25 9 17.91 448.75 783.41 25 10 13.32 399.24 552.3 23 11 13.32 399.24 529.37 23 12 13.32 399.24 666.43 23 13 23.29 786.42 742.41 32 14 23.29 786.42 855.49 31 15 23.29 786.42 926.53 34 16 22.44 751.41 1146.63 38 17 22.44 751.41 974.55 38 18 22.44 751.41 1075.59 38 19 15.89 572.32 630.36 25 20 15.89 572.32 743.44 26 21 15.89 572.32 872.48 25 22 10.67 384.7 537.3 20.5 23 10.67 384.7 624.34 18.5 24 10.67 384.7 681.36 19.5 25 15.29 447.77 430.3 25 26 15.29 447.77 593.37 25 27 15.29 447.77 694.41 25 28 16.64 597.78 702.35 29 29 16.64 597.78 849.42 29 30 16.64 597.78 980.46 27 31 18.52 826.89 646.35 41 32 18.52 826.89 809.42 41 33 18.52 826.89 924.44 41 34 19.2 598.83 807.5 31 35 19.2 598.83 904.55 22 36 19.2 598.83 452.78 25 37 15.89 595.81 694.41 33 38 15.89 595.81 416.24 35 39 15.89 595.81 464.77 28 40 19.1 598.35 650.4 29 41 19.1 598.35 797.47 28 42 19.1 598.35 868.5 28 43 4.97 562.27 616.29 30 44 4.97 562.27 745.34 30 45 4.97 562.27 873.39 30 46 12.85 415.24 492.29 23 47 12.85 415.24 629.35 23 48 12.85 415.24 716.38 23 49 17.9 454.78 637.39 25 50 17.9 454.78 708.43 25 51 17.9 454.78 821.51 25 52 14.32 449.76 522.3 25 53 14.32 449.76 621.37 25 54 14.32 449.76 660.41 25 55 1.53 338.19 319.2 20 56 1.53 338.19 448.24 20 57 1.53 338.19 576.3 20 58 14.16 510.78 451.27 24 59 14.16 510.78 564.35 25 60 14.16 510.78 763.45 27 61 19.45 744.72 845.39 43 62 19.45 744.72 789.37 41 63 19.45 744.72 917.47 40 64 22.56 717.43 611.35 30 65 22.56 478.62 611.35 16 66 22.56 478.62 407.9 19 67 19.53 655.98 559.34 34 68 19.53 655.98 763.43 27 69 19.53 655.98 891.49 25 70 12.98 579.26 641.33 31 71 12.98 579.26 827.4 29 72 12.98 579.26 928.45 27 73 16.92 457.77 416.26 22 74 16.92 457.77 517.31 21 75 16.92 457.77 687.41 22 76 27.6 728.74 788.89 29 77 27.6 728.74 845.51 31 78 27.6 728.74 1008.57 31 79 26.39 803.11 1028.61 35 80 26.39 803.11 799.5 30 81 26.39 803.11 957.57 35 82 11.46 597.28 522.18 26 83 11.46 597.28 672.37 33 84 11.46 597.28 901.44 26 85 26.58 822.81 604.87 30 86 26.58 822.81 688.91 26 87 26.58 822.81 998.59 39 88 19.29 754.93 598.33 30 89 19.29 754.93 817.43 45 90 19.29 754.93 1027.57 38 91 18.18 560.29 476.27 30 92 18.18 560.29 589.36 30 93 18.18 560.29 775.43 30 94 13.88 411.74 305.18 23 95 13.88 411.74 531.35 23 96 13.88 411.74 659.41 23 97 9.97 423.23 458.31 25 98 9.97 423.23 572.35 23 99 9.97 423.23 701.39 21 100 19.92 388.74 435.27 19 101 19.92 388.74 548.36 17 102 19.92 388.74 663.38 19 103 5.57 540.28 373.21 35 104 5.57 540.28 829.41 26 105 5.57 540.28 483.74 29 106 10.45 441.72 564.31 23 107 10.45 441.72 651.35 22 108 10.45 441.72 738.38 21 109 4.52 367.19 434.22 21 110 4.52 367.19 549.25 17 111 4.52 367.19 662.34 18 112 21.88 803.84 1100.48 41 113 21.88 803.84 730.31 38 114 21.88 803.84 613.27 46 115 20.03 728.9 550.3 39 116 20.03 728.9 834.47 41 117 20.03 728.9 962.53 39 118 16.81 672.3 769.35 26 119 16.81 672.3 882.44 26 120 16.81 672.3 969.47 26 121 13.59 351.23 444.32 18 122 13.59 351.23 543.39 16 123 13.59 351.23 614.42 17 124 14.51 503.27 720.4 28 125 14.51 503.27 817.45 19 126 14.51 503.27 409.23 20 127 22.39 722.92 428.29 37 128 22.39 722.92 854.53 37 129 22.39 722.92 955.58 37 130 12.77 434.23 565.33 24 131 12.77 434.23 739.4 21 132 12.77 434.23 796.42 22 133 12.41 477.73 553.27 27 134 12.41 477.73 713.3 26 135 12.41 477.73 770.33 24 136 7.63 388.2 476.24 22 137 7.63 388.2 547.27 19 138 7.63 388.2 662.3 19 139 12.85 375.7 343.21 22 140 12.85 375.7 474.25 22 141 12.85 375.7 637.31 22 142 20.72 403.74 397.28 23 143 20.72 403.74 560.34 23 144 20.72 403.74 659.41 23 145 19.66 542.34 600.37 23 146 19.66 542.34 671.41 25 147 19.66 542.34 871.52 23 148 22.14 939.94 1180.52 46 149 22.14 939.94 540.27 46 150 22.14 939.94 802.36 46 151 12.66 392.18 409.19 22 152 12.66 392.18 523.24 22 153 12.66 392.18 620.29 22

TABLE 5 inlet potential Potential at Transition Orifice before collision cell Positivity number potential Q0 outlet threshold 1 80 10 35 2000 2 80 10 35 2000 3 80 10 35 2000 4 80 10 35 1400 5 80 10 35 2000 6 80 10 35 2000 7 80 10 35 2000 8 80 10 35 2000 9 80 10 35 1500 10 80 10 35 4000 11 80 10 35 4000 12 80 10 35 4000 13 120 10 18 2000 14 120 10 18 2000 15 120 10 18 2000 16 80 10 35 2000 17 80 10 35 2000 18 80 10 35 2000 19 90 10 15 2000 20 90 10 15 2000 21 90 10 15 2000 22 85 10 24 2000 23 85 10 24 2000 24 85 10 24 2000 25 80 10 35 2000 26 80 10 35 1500 27 80 10 35 2000 28 100 10 17 2000 29 100 10 17 2000 30 100 10 17 2000 31 80 10 35 1000 32 80 10 35 2000 33 80 10 35 2000 34 105 10 20 1400 35 105 10 20 2000 36 105 10 20 2000 37 100 10 11 2000 38 100 10 16 2000 39 100 10 11 2000 40 90 10 16 2000 41 90 10 18 2000 42 90 10 22 2000 43 80 10 35 2000 44 80 10 35 2000 45 80 10 35 2000 46 80 10 35 2000 47 80 10 35 2000 48 80 10 35 2000 49 80 10 35 2000 50 80 10 35 2000 51 80 10 35 2000 52 80 10 35 2000 53 80 10 35 2000 54 80 10 35 2000 55 80 10 35 2000 56 80 10 35 2000 57 80 10 35 2000 58 75 12 11 2000 59 75 12 14 2000 60 75 12 18 2000 61 140 10 35 2000 62 140 10 35 2000 63 140 10 35 2000 64 120 10 35 2000 65 70 10 35 2000 66 70 10 35 2000 67 100 10 35 2000 68 100 10 35 2000 69 100 10 35 2000 70 80 12 15 2000 71 80 12 19 2000 72 80 12 22 2000 73 70 12 10 4000 74 70 12 13 4000 75 70 12 16 4000 76 120 10 35 2000 77 120 10 35 2000 78 120 10 35 2000 79 120 10 35 2000 80 120 10 35 2000 81 120 10 35 2000 82 85 12 13 2000 83 85 12 16 2000 84 85 12 21 2000 85 100 10 35 2000 86 100 10 35 2000 87 100 10 35 2000 88 100 10 35 2000 89 100 10 35 2000 90 100 10 35 2000 91 80 10 35 2000 92 80 10 35 2000 93 80 10 35 2000 94 80 10 35 2000 95 80 10 35 2000 96 80 10 35 2000 97 75 10 11 2000 98 75 10 14 2000 99 75 10 16 1800 100 140 6 10 1300 101 140 6 14 2000 102 140 6 16 2000 103 110 12 10 2000 104 110 12 20 2000 105 110 12 6 2000 106 75 12 14 2000 107 75 12 16 2000 108 75 12 18 2000 109 65 12 18 2000 110 65 12 23 2000 111 65 12 15 2000 112 100 10 35 2000 113 100 10 35 2000 114 100 10 35 2000 115 140 9 14 2000 116 140 9 34 2000 117 140 9 24 2000 118 125 9 18 2000 119 125 9 21 2000 120 125 9 41 2000 121 70 12 10 2000 122 70 12 23 2000 123 70 12 14 2000 124 70 12 17 8000 125 70 12 20 2000 126 70 12 10 2000 127 80 10 35 2000 128 80 10 35 2000 129 80 10 35 2000 130 70 12 14 2000 131 70 12 18 2000 132 70 12 19 2000 133 80 12 14 2000 134 80 12 18 2000 135 80 12 18 2000 136 70 12 12 1600 137 70 12 13 2000 138 70 12 16 2000 139 80 10 35 2000 140 80 10 35 2000 141 80 10 35 2000 142 80 10 35 2000 143 80 10 35 2000 144 80 10 35 2000 145 80 12 16 2000 146 80 12 14 2000 147 80 12 21 2000 148 80 10 35 2000 149 80 10 35 2000 150 80 10 35 2000 151 80 10 35 3000 152 80 10 35 2000 153 80 10 35 2000

-   -   The other machine variables used are as follows:         -   Type of scan: MRM         -   MRM planned: yes         -   Polarity: Positive         -   Ionization source: Turbo V™ (Applied BioSystems)         -   Q1 setting: Filtering with unit resolution         -   Q3 setting: Filtering with unit resolution         -   Inter-scan pause: 5.00 ms         -   Scanning speed: 10 Da/s         -   Curtain gas: 50.00 psi         -   Cone voltage: 5500.00 V         -   Source temperature: 550.00° C.         -   Spraying gas: 50.00 psi         -   Heating gas: 40.00 psi         -   Collision gas inducing dissociation: 9.00 psi         -   Dynamic filling: inactivated         -   Total cycle time: 1.2 s         -   Detection window: 90 s

The areas obtained for each of the transitions and for each of the microorganisms investigated were measured. When the area of a transition is greater than or equal to the positivity threshold described in TABLE 5, detection of the transition is regarded as positive and is marked “1” in TABLE 6. When the area of a transition is below the positivity threshold described in TABLE 5, detection of the transition is regarded as negative and is marked “0” in TABLE 6. When the 3 transitions of one and the same peptide are marked “1”, detection of the peptide is regarded as positive. One particular case is an exception to this rule. The peptide corresponding to the transitions with numbers 49, 50 and 51 has a transition of very low intensity. In this precise case, when transitions 49 and 50 are marked “1”, detection of this peptide will be regarded as positive.

TABLE 6 Transition number Smp1 Smp2 Smp3 Smp4 Smp5 Smp6 Smp7 Smp8 Smp9 Smp10 Smp11 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 0 0 0 1 0 6 0 0 0 0 0 0 0 0 0 1 0 7 0 0 0 0 0 0 0 0 0 1 0 8 0 0 0 0 0 0 0 0 0 1 0 9 0 0 0 0 0 0 0 0 0 1 0 10 0 0 0 0 0 0 0 0 0 1 0 11 0 0 0 0 0 0 0 0 0 1 0 12 0 0 0 0 0 0 0 0 0 1 0 13 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1 0 0 0 0 0 0 1 1 20 0 0 1 0 0 0 0 0 0 1 1 21 0 0 1 0 0 0 0 0 0 1 1 22 0 0 1 0 0 0 0 0 0 1 0 23 0 0 1 0 0 0 0 0 0 1 0 24 0 0 1 0 0 0 0 0 0 1 0 25 0 0 0 0 0 0 0 0 0 1 0 26 0 0 0 0 0 0 0 0 0 1 0 27 0 0 0 0 0 0 0 0 0 1 0 28 0 0 0 0 0 0 0 0 0 1 0 29 0 0 0 0 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 0 0 1 0 32 0 0 0 0 0 0 0 0 0 1 0 33 0 0 0 0 0 0 0 0 0 1 0 34 0 0 1 0 0 0 0 0 0 1 1 35 0 0 1 0 0 0 0 0 0 1 1 36 0 0 1 0 0 0 0 0 0 1 1 37 0 0 0 0 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0 0 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 0 0 0 0 41 0 0 0 0 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0 0 0 0 48 0 0 0 0 0 0 0 0 0 0 0 49 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 0 51 0 0 0 0 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 0 0 0 0 54 0 0 0 0 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 0 0 0 1 60 0 0 0 0 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 0 0 0 0 73 0 0 0 0 0 0 0 0 0 0 0 74 0 0 0 0 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 0 0 0 0 76 0 0 0 0 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 0 0 0 0 80 0 1 0 0 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 0 0 0 0 93 0 0 0 0 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 0 0 0 0 97 0 0 0 0 0 0 0 0 1 0 0 98 0 0 0 0 0 0 0 0 1 0 0 99 0 0 0 0 0 0 0 0 1 0 0 100 0 0 0 0 0 0 0 0 1 0 0 101 0 0 0 0 0 0 0 0 1 0 0 102 0 0 0 0 0 0 0 0 1 0 0 103 0 0 0 0 0 0 0 0 0 0 0 104 0 0 0 0 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 0 0 0 0 106 0 0 0 0 0 0 0 0 1 0 0 107 0 0 0 0 0 0 0 0 1 0 0 108 0 0 0 0 0 0 0 0 1 0 0 109 0 0 0 0 0 0 0 0 0 0 0 110 0 0 0 0 0 0 0 0 0 0 0 111 0 0 0 0 0 0 0 0 0 0 0 112 0 0 0 0 0 0 0 0 0 0 0 113 0 0 0 0 0 0 0 0 0 0 0 114 0 0 0 0 0 0 0 0 0 0 0 115 0 0 0 0 0 0 0 0 0 0 0 116 0 0 0 0 0 0 0 0 0 0 0 117 0 0 0 0 0 0 0 0 0 0 0 118 0 0 0 0 0 0 0 0 0 1 0 119 0 0 0 0 0 0 0 0 0 1 0 120 0 1 0 0 0 0 0 0 0 0 0 121 0 0 0 0 0 0 1 0 0 0 0 122 0 0 0 0 0 0 0 0 0 0 0 123 0 0 0 0 0 0 0 0 0 0 0 124 0 0 0 0 0 0 0 0 0 0 0 125 1 0 1 0 0 1 0 0 0 0 0 126 1 0 1 0 0 1 0 0 0 0 0 127 0 0 0 0 0 0 0 0 0 0 0 128 0 0 0 0 0 0 0 0 0 0 0 129 0 0 0 0 0 0 0 0 0 0 0 130 0 0 0 0 0 0 0 0 0 0 0 131 0 0 0 0 0 1 0 0 0 0 0 132 0 0 0 0 0 0 0 0 0 0 0 133 0 0 0 0 0 0 0 0 0 0 0 134 0 0 0 0 0 0 0 0 0 0 0 135 0 0 0 0 0 0 0 0 0 0 0 136 0 0 0 0 0 1 0 0 0 0 0 137 0 0 0 0 0 1 1 0 0 0 0 138 0 0 0 0 0 1 0 0 0 0 0 139 0 0 0 0 0 0 0 0 0 0 0 140 0 0 0 0 0 0 0 0 0 0 0 141 0 0 0 0 0 0 0 0 0 0 0 142 0 0 0 0 0 0 0 0 0 0 0 143 0 0 0 0 0 0 0 0 0 0 0 144 0 0 0 0 0 0 0 0 0 0 0 145 0 0 0 0 0 1 0 0 0 0 0 146 0 0 0 0 0 1 0 0 0 0 0 147 0 0 0 0 0 1 0 0 0 0 0 148 0 0 0 0 0 0 0 0 0 0 0 149 0 0 0 0 0 0 0 0 0 0 0 150 0 0 0 0 0 0 0 0 0 0 0 151 0 0 1 0 0 0 0 0 0 0 0 152 0 0 1 0 0 0 0 0 0 0 0 153 0 0 1 0 0 0 0 0 0 0 0

Samples Smp1, Smp2, Smp4, Smp5, Smp7 and Smp9 do not have any peptide characteristic of resistance of the Van type. The bacteria present in samples Smp1, Smp2, Smp4, Smp5, Smp7 and Smp9 may be sensitive to the glycopeptides of the vancomycin or teicoplanin type.

Samples Smp3, Smp10 and Smp11 comprise at least one peptide characteristic of VanA. The bacteria present in samples Smp3, Smp10 and Smp11 therefore express the ligase VanA, which endows them with resistance to vancomycin and to teicoplanin.

Sample Smp6 comprises at least one peptide characteristic of VanG. The bacterium present in sample Smp6 therefore expresses the ligase VanG, which endows it with resistance to vancomycin.

Sample Smp8 comprises at least one peptide characteristic of VanD. The bacterium present in sample Smp8 therefore expresses the ligase VanD, which endows it with resistance to vancomycin and to teicoplanin.

Thus, advantageously, several mechanisms of resistance to glycopeptides are investigated simultaneously. Particularly advantageously, a mechanism of inducible resistance, such as the mechanism of resistance linked to expression of VanA, is detected without an induction phase during culture of the microorganism. This method therefore makes it possible to investigate the mechanisms of resistance to glycopeptides without a priori on their possible existence.

EXAMPLE 9 Identification of Resistance to Glycopeptides, with Induction, of Type VanA, VanB, VanD, VanE and VanG

Samples Smp1 to Smp11 are identified according to one of the methods described in examples 1 to 6. Identification of the species is reported in TABLE 7.

TABLE 7 Name Species Smp12 E. faecalis Smp13 E. faecalis Smp14 E. faecalis Smp15 E. faecalis Smp16 E. faecalis Smp17 E. faecium Smp18 E. faecium Smp19 E. faecalis Smp20 E. faecium Samples Smp12 to Smp20 correspond to a species that may comprise a mechanism of resistance of the Van type. The following method is then employed for investigating such a mechanism.

The microorganism colony is obtained according to example 3 and then treated according to example 7 and analyzed according to example 8.

The areas obtained for each of the transitions and for each of the microorganisms studied were measured. When the area of a transition is greater than or equal to the positivity threshold described in TABLE 5, detection of the transition is regarded as positive and is marked “1” in TABLE 8. When the area of a transition is below the positivity threshold described in TABLE 5, detection of the transition is regarded as negative and is marked “0” in TABLE 8. When the 3 transitions of one and the same peptide are marked “1”, detection of the peptide is regarded as positive. One particular case is an exception to this rule. The peptide corresponding to the transitions numbered 49, 50 and 51 has a transition of very low intensity. In this precise case, when the transitions 49 and 50 are marked “1”, detection of this peptide will be regarded as positive.

TABLE 8 Transition number Smp12 Smp13 Smp14 Smp15 Smp16 Smp17 Smp18 Smp19 Smp20 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 1 0 4 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 1 6 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 1 1 8 0 0 0 0 0 0 0 1 1 9 0 0 0 0 0 0 0 1 1 10 0 0 0 0 0 0 0 1 1 11 0 0 0 0 0 0 0 1 1 12 0 0 0 0 0 0 0 1 1 13 0 0 0 0 0 0 0 1 1 14 0 0 0 0 0 0 0 1 1 15 0 0 0 0 0 0 0 1 1 16 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 1 1 20 0 0 0 0 0 0 0 1 1 21 0 0 0 0 0 0 0 1 1 22 0 0 0 0 0 0 0 1 1 23 0 0 0 0 0 0 0 1 1 24 0 0 0 0 0 0 0 1 1 25 0 0 0 1 0 0 0 1 0 26 0 0 0 0 0 0 0 1 0 27 0 0 0 0 0 0 0 1 0 28 0 0 0 0 0 0 0 1 1 29 0 0 0 0 0 0 0 1 1 30 0 0 0 0 0 0 0 1 1 31 0 0 0 0 0 0 0 1 1 32 0 0 0 0 0 0 0 1 0 33 0 0 0 0 0 0 0 1 0 34 0 0 0 0 0 0 0 1 1 35 0 0 0 0 0 0 0 1 1 36 0 0 0 0 0 0 0 1 1 37 0 1 1 0 0 0 0 0 0 38 0 1 1 0 0 0 0 0 0 39 0 1 1 0 0 0 1 0 0 40 0 1 1 0 0 0 1 0 0 41 0 1 1 0 0 0 0 0 0 42 0 1 1 0 0 0 0 0 0 43 0 0 0 0 0 0 0 0 0 44 0 0 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 0 0 46 0 1 1 0 0 1 1 0 0 47 0 1 1 0 0 0 1 0 0 48 0 1 1 0 0 0 1 0 0 49 0 1 1 0 0 0 0 0 0 50 0 1 1 0 0 0 0 0 0 51 0 0 0 0 0 0 0 0 0 52 0 0 0 0 0 0 0 0 0 53 0 0 0 0 0 0 0 0 0 54 0 1 0 0 0 0 0 0 0 55 0 0 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 0 0 58 0 0 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0 0 0 61 0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 0 0 64 0 0 0 0 0 0 0 0 0 65 0 0 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 0 0 69 0 0 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 0 0 72 0 0 0 0 0 0 0 0 0 73 0 0 0 0 0 1 0 0 0 74 0 0 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 0 0 76 0 0 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 0 0 78 0 0 0 0 0 0 0 0 0 79 0 0 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 0 0 81 0 0 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 0 0 83 0 0 0 0 0 0 0 0 0 84 0 0 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 0 0 93 0 0 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 0 0 97 0 0 0 0 0 1 0 0 0 98 0 0 0 0 0 1 0 0 0 99 0 0 0 0 0 1 0 0 0 100 0 0 0 0 0 1 0 0 0 101 0 0 0 0 0 1 0 0 0 102 0 0 0 0 0 1 0 0 1 103 0 0 0 0 0 0 0 0 0 104 0 0 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 0 0 106 0 0 0 0 0 1 0 0 0 107 0 0 0 0 0 1 0 0 0 108 0 0 0 0 0 1 0 0 0 109 0 0 0 0 0 0 0 0 0 110 0 0 0 0 1 0 0 0 0 111 0 0 0 0 0 0 0 0 0 112 0 0 0 0 0 0 0 0 0 113 0 0 0 0 0 0 0 0 0 114 0 0 0 0 0 0 0 0 0 115 0 0 0 0 0 0 0 0 0 116 0 0 0 0 0 0 0 0 0 117 0 0 0 0 0 0 0 0 0 118 0 0 0 0 0 0 0 0 0 119 0 0 0 0 0 0 0 0 0 120 0 0 0 0 0 0 0 0 0 121 0 0 0 0 1 0 0 0 0 122 0 0 0 0 1 0 0 0 0 123 0 0 0 0 1 0 0 0 0 124 0 0 0 0 0 0 0 0 0 125 0 0 1 0 1 0 0 0 0 126 0 0 1 0 1 0 0 0 0 127 0 0 0 0 0 1 0 0 0 128 0 0 0 0 0 1 0 0 0 129 0 0 0 0 0 0 0 0 0 130 0 0 0 1 0 0 0 0 0 131 0 0 0 1 0 0 0 0 0 132 0 0 0 1 0 0 0 0 0 133 0 0 0 1 0 0 0 0 0 134 0 0 0 1 0 0 0 0 0 135 0 0 0 1 0 0 0 0 0 136 0 0 0 1 0 0 0 0 0 137 0 0 0 1 0 0 0 0 0 138 0 0 0 1 0 0 0 0 0 139 0 0 0 1 0 0 0 0 0 140 0 0 0 1 0 0 0 0 0 141 0 0 0 1 0 0 0 0 0 142 0 0 0 0 0 0 0 0 0 143 0 0 0 0 0 0 0 0 0 144 0 0 0 0 0 0 0 0 0 145 0 0 0 1 0 0 0 0 0 146 0 0 0 1 0 0 0 0 0 147 0 0 0 1 0 0 0 0 0 148 0 0 0 0 0 0 0 0 0 149 0 0 0 0 0 0 0 0 0 150 0 0 0 0 0 0 0 0 0 151 0 0 0 1 0 0 0 0 0 152 0 0 0 1 0 0 0 0 0 153 0 0 0 1 0 0 0 0 0

Sample Smp12 does not have any peptide characteristic of resistance of the Van type. The bacterium present in sample Smp12 may be sensitive to the glycopeptides of the vancomycin or teicoplanin type.

Samples Smp19 and Smp20 comprise at least one peptide characteristic of VanA. The bacteria present in samples Smp19 and Smp20 therefore express the ligase VanA, which endows them with resistance to vancomycin and to teicoplanin.

Samples Smp13, Smp14 and Smp18 comprise at least one peptide characteristic of VanB. The bacteria present in samples Smp13, Smp14 and Smp18 therefore express the ligase VanB, which endows them with resistance to vancomycin.

Sample Smp15 comprises at least one peptide characteristic of VanG. The bacterium present in sample Smp15 expresses the ligase VanG, which endows it with resistance to vancomycin.

Sample Smp16 comprises at least one peptide characteristic of VanE. The bacterium present in sample Smp16 expresses the ligase VanE, which endows it with resistance to vancomycin.

Sample Smp17 comprises at least one peptide characteristic of VanD. The bacterium present in sample Smp17 expresses the ligase VanD, which endows it with resistance to vancomycin and to teicoplanin.

Thus, advantageously, several mechanisms of resistance to glycopeptides may be investigated simultaneously.

EXAMPLE 10 Obtaining Digested Proteins from Microorganisms

The following protocol is carried out in 16 steps:

-   -   1. Taking a sample of a microorganism colony, obtained according         to example 8 and suspended in 100 μl of a solution of ammonium         bicarbonate, 50 mM, pH=8.0 in a tube containing glass beads with         diameter from 0.05 mm to 2 mm     -   2. Addition of dithiothreitol (DTT) to obtain a final         concentration of 5 mM.     -   3. Reduction for 5 minutes at 95° C. on a Hielscher probe         (instrument settings: amplitude: 100, cycle: 1)     -   4. Cooling of the tubes to room temperature.     -   5. Addition of iodoacetamide to obtain a final concentration of         12.5 mM.     -   6. Alkylation for 5 minutes at room temperature and away from         the light.     -   7. Addition of 1 μg of trypsin.     -   8. Digestion at 50° C. for 15 minutes     -   9. Addition of formic acid until the pH is below 4 to stop the         reaction.     -   10. Centrifugation for 5 minutes at 15 000 g, the supernatant is         recovered and made up to 1 mL with water/formic acid 0.5% (v/v)     -   11. Equilibration of the Waters Oasis HLB columns with 1 ml of         methanol and then 1 ml H₂O/formic acid 0.1% (v/v)     -   12. Deposition of the sample, which flows by gravity     -   13. Washing with 1 ml H₂O/formic acid 0.1% (v/v)     -   14. Elution with 1 ml of a mixture of 80% methanol and 20%         water/formic acid 0.1% (v/v)     -   15. The eluate is evaporated with an evaporator of the SpeedVac®         SPD2010 type (Thermo Electron Corporation, Waltham, Mass.,         United States of America), for 2 hours, in order to obtain a         volume of about 100 μl.     -   16. The eluate is then taken up in a solution of water/formic         acid 0.5% (v/v), sufficient quantity (Q.S.) for 150 μl

EXAMPLE 11 Identification of Resistance to Glycopeptides, without induction, of Type VanA

Samples Smp21 and Smp22 are identified according to one of the methods described in examples 1 to 6. Identification of the species is reported in TABLE 9.

TABLE 9 Name Species Smp21 E. faecalis Smp22 E. faecalis Samples Smp21 and Smp22 correspond to the species Enterococcus faecalis, which may comprise a mechanism of resistance of the Van type. The following method is then employed for investigating such a mechanism.

Each sample is treated according to example 10 and analyzed according to example 8 apart from the elements mentioned below.

-   -   The transitions mentioned in TABLE 3 are detected using the         parameters shown in TABLES 10 and 11.

TABLE 10 (m/z) (m/z) Collision Transition Retention filtered in filtered in energy number time Q1 Q3 (eV) 1 8.75 554.79 601.32 29 2 8.75 554.79 730.36 29 3 8.75 554.79 858.42 29 4 19.71 385.28 444.32 22 5 19.71 385.28 543.39 22 6 19.71 385.28 656.47 22 7 17.91 448.75 492.29 25 8 17.91 448.75 655.36 25 9 17.91 448.75 783.41 25 10 13.32 399.24 552.3 23 11 13.32 399.24 529.37 23 12 13.32 399.24 666.43 23 13 23.29 786.42 742.41 32 14 23.29 786.42 855.49 31 15 23.29 786.42 926.53 34 16 22.44 751.41 1146.63 38 17 22.44 751.41 974.55 38 18 22.44 751.41 1075.59 38 19 15.89 572.32 630.36 25 20 15.89 572.32 743.44 26 21 15.89 572.32 872.48 25 22 10.67 384.7 537.3 20.5 23 10.67 384.7 624.34 18.5 24 10.67 384.7 681.36 19.5 25 15.29 447.77 430.3 25 26 15.29 447.77 593.37 25 27 15.29 447.77 694.41 25 28 16.64 597.78 702.35 29 29 16.64 597.78 849.42 29 30 16.64 597.78 980.46 27 31 18.52 826.89 646.35 41 32 18.52 826.89 809.42 41 33 18.52 826.89 924.44 41 34 19.2 598.83 807.5 31 35 19.2 598.83 904.55 22 36 19.2 598.83 452.78 25 37 15.89 595.81 694.41 33 38 15.89 595.81 416.24 35 39 15.89 595.81 464.77 28 40 19.1 598.35 650.4 29 41 19.1 598.35 797.47 28 42 19.1 598.35 868.5 28 43 4.97 562.27 616.29 30 44 4.97 562.27 745.34 30 45 4.97 562.27 873.39 30 46 12.85 415.24 492.29 23 47 12.85 415.24 629.35 23 48 12.85 415.24 716.38 23 49 17.9 454.78 637.39 25 50 17.9 454.78 708.43 25 51 17.9 454.78 821.51 25 52 14.32 449.76 522.3 25 53 14.32 449.76 621.37 25 54 14.32 449.76 660.41 25 55 1.53 338.19 319.2 20 56 1.53 338.19 448.24 20 57 1.53 338.19 576.3 20 58 14.16 510.78 451.27 24 59 14.16 510.78 564.35 25 60 14.16 510.78 763.45 27 61 19.45 744.72 845.39 43 62 19.45 744.72 789.37 41 63 19.45 744.72 917.47 40 64 22.56 717.43 611.35 30 65 22.56 478.62 611.35 16 66 22.56 478.62 407.9 19 67 19.53 655.98 559.34 34 68 19.53 655.98 763.43 27 69 19.53 655.98 891.49 25 70 12.98 579.26 641.33 31 71 12.98 579.26 827.4 29 72 12.98 579.26 928.45 27 73 16.92 457.77 416.26 22 74 16.92 457.77 517.31 21 75 16.92 457.77 687.41 22 76 27.6 728.74 788.89 29 77 27.6 728.74 845.51 31 78 27.6 728.74 1008.57 31 79 26.39 803.11 1028.61 35 80 26.39 803.11 799.5 30 81 26.39 803.11 957.57 35 82 11.46 597.28 522.18 26 83 11.46 597.28 672.37 33 84 11.46 597.28 901.44 26 85 26.58 822.81 604.87 30 86 26.58 822.81 688.91 26 87 26.58 822.81 998.59 39 88 19.29 754.93 598.33 30 89 19.29 754.93 817.43 45 90 19.29 754.93 1027.57 38 91 18.18 560.29 476.27 30 92 18.18 560.29 589.36 30 93 18.18 560.29 775.43 30 94 13.88 411.74 305.18 23 95 13.88 411.74 531.35 23 96 13.88 411.74 659.41 23 97 9.97 423.23 458.31 25 98 9.97 423.23 572.35 23 99 9.97 423.23 701.39 21 100 19.92 388.74 435.27 19 101 19.92 388.74 548.36 17 102 19.92 388.74 663.38 19 103 5.57 540.28 373.21 35 104 5.57 540.28 829.41 26 105 5.57 540.28 483.74 29 106 10.45 441.72 564.31 23 107 10.45 441.72 651.35 22 108 10.45 441.72 738.38 21 109 4.52 367.19 434.22 21 110 4.52 367.19 549.25 17 111 4.52 367.19 662.34 18 112 21.88 803.84 1100.48 41 113 21.88 803.84 730.31 38 114 21.88 803.84 613.27 46 115 20.03 728.9 550.3 39 116 20.03 728.9 834.47 41 117 20.03 728.9 962.53 39 118 16.81 672.3 769.35 26 119 16.81 672.3 882.44 26 120 16.81 672.3 969.47 26 121 13.59 351.23 444.32 18 122 13.59 351.23 543.39 16 123 13.59 351.23 614.42 17 124 14.51 503.27 720.4 28 125 14.51 503.27 817.45 19 126 14.51 503.27 409.23 20 127 22.39 722.92 428.29 37 128 22.39 722.92 854.53 37 129 22.39 722.92 955.58 37 130 12.77 434.23 565.33 24 131 12.77 434.23 739.4 21 132 12.77 434.23 796.42 22 133 12.41 477.73 553.27 27 134 12.41 477.73 713.3 26 135 12.41 477.73 770.33 24 136 7.63 388.2 476.24 22 137 7.63 388.2 547.27 19 138 7.63 388.2 662.3 19 139 12.85 375.7 343.21 22 140 12.85 375.7 474.25 22 141 12.85 375.7 637.31 22 142 20.72 403.74 397.28 23 143 20.72 403.74 560.34 23 144 20.72 403.74 659.41 23 145 19.66 542.34 600.37 23 146 19.66 542.34 671.41 25 147 19.66 542.34 871.52 23 148 22.14 939.94 1180.52 46 149 22.14 939.94 540.27 46 150 22.14 939.94 802.36 46 151 12.66 392.18 409.19 22 152 12.66 392.18 523.24 22 153 12.66 392.18 620.29 22

TABLE 11 inlet potential Potential at Transition Orifice before collision cell Positivity number potential Q0 outlet threshold 1 80 10 35 2000 2 80 10 35 2000 3 80 10 35 2000 4 80 10 35 600 5 80 10 35 2000 6 80 10 35 1000 7 80 10 35 2000 8 80 10 35 2000 9 80 10 35 2000 10 80 10 35 2000 11 80 10 35 2000 12 80 10 35 2000 13 120 10 18 2000 14 120 10 18 2000 15 120 10 18 2000 16 80 10 35 2000 17 80 10 35 2000 18 80 10 35 2000 19 90 10 15 2000 20 90 10 15 2000 21 90 10 15 2000 22 85 10 24 2000 23 85 10 24 2000 24 85 10 24 2000 25 80 10 35 2000 26 80 10 35 2000 27 80 10 35 2000 28 100 10 17 2000 29 100 10 17 2000 30 100 10 17 2000 31 80 10 35 2000 32 80 10 35 2000 33 80 10 35 2000 34 105 10 20 2000 35 105 10 20 2000 36 105 10 20 2000 37 100 10 11 2000 38 100 10 16 2000 39 100 10 11 2000 40 90 10 16 2000 41 90 10 18 2000 42 90 10 22 2000 43 80 10 35 2000 44 80 10 35 2000 45 80 10 35 2000 46 80 10 35 2000 47 80 10 35 2000 48 80 10 35 2000 49 80 10 35 2000 50 80 10 35 2000 51 80 10 35 2000 52 80 10 35 2000 53 80 10 35 2000 54 80 10 35 2000 55 80 10 35 2000 56 80 10 35 2000 57 80 10 35 2000 58 75 12 11 2000 59 75 12 14 2000 60 75 12 18 2000 61 140 10 35 2000 62 140 10 35 2000 63 140 10 35 2000 64 120 10 35 2000 65 70 10 35 2000 66 70 10 35 2000 67 100 10 35 2000 68 100 10 35 2000 69 100 10 35 2000 70 80 12 15 3500 71 80 12 19 2500 72 80 12 22 4500 73 70 12 10 2000 74 70 12 13 2000 75 70 12 16 2000 76 120 10 35 2000 77 120 10 35 2000 78 120 10 35 2000 79 120 10 35 2000 80 120 10 35 2000 81 120 10 35 2000 82 85 12 13 2000 83 85 12 16 2000 84 85 12 21 2000 85 100 10 35 2000 86 100 10 35 2000 87 100 10 35 2000 88 100 10 35 2000 89 100 10 35 4000 90 100 10 35 2000 91 80 10 35 4000 92 80 10 35 3500 93 80 10 35 6000 94 80 10 35 2000 95 80 10 35 2000 96 80 10 35 2000 97 75 10 11 2000 98 75 10 14 2000 99 75 10 16 2000 100 140 6 10 2000 101 140 6 14 2000 102 140 6 16 2000 103 110 12 10 2000 104 110 12 20 2000 105 110 12 6 2000 106 75 12 14 2000 107 75 12 16 2000 108 75 12 18 2000 109 65 12 18 2000 110 65 12 23 2000 111 65 12 15 2000 112 100 10 35 2000 113 100 10 35 2000 114 100 10 35 2000 115 140 9 14 2000 116 140 9 34 2000 117 140 9 24 2000 118 125 9 18 2000 119 125 9 21 2000 120 125 9 41 2000 121 70 12 10 2000 122 70 12 23 2000 123 70 12 14 2000 124 70 12 17 2500 125 70 12 20 2500 126 70 12 10 2500 127 80 10 35 2000 128 80 10 35 2000 129 80 10 35 2000 130 70 12 14 2000 131 70 12 18 2000 132 70 12 19 2000 133 80 12 14 2000 134 80 12 18 2000 135 80 12 18 2000 136 70 12 12 2000 137 70 12 13 2000 138 70 12 16 2000 139 80 10 35 2000 140 80 10 35 2000 141 80 10 35 2000 142 80 10 35 2000 143 80 10 35 2000 144 80 10 35 2000 145 80 12 16 2000 146 80 12 14 2000 147 80 12 21 2000 148 80 10 35 2000 149 80 10 35 2000 150 80 10 35 2000 151 80 10 35 2800 152 80 10 35 2000 153 80 10 35 2000

-   -   The other machine variables used are as follows:         -   Type of scan: MRM         -   MRM planned: yes         -   Polarity: Positive         -   Ionization source: Turbo V™ (Applied BioSystems)         -   Setting Q1: Filtering with unit resolution         -   Setting Q3: Filtering with unit resolution         -   Inter-scan pause: 5.00 ms         -   Scanning speed: 10 Da/s         -   Curtain gas: 50.00 psi         -   Cone voltage: 5500.00 V         -   Source temperature: 550.00° C.         -   Spraying gas: 50.00 psi         -   Heating gas: 40.00 psi         -   Collision gas inducing dissociation: 9.00 psi         -   Dynamic filling: inactivated         -   Total cycle time: 1.2 s         -   Detection window: 90 s

The areas obtained for each of the transitions and for each of the microorganisms studied were measured. When the area of a transition is greater than or equal to the positivity threshold described in TABLE 11, detection of the transition is regarded as positive and is marked “1” in TABLE 12. When the area of a transition is below the positivity threshold described in TABLE 11, detection of the transition is regarded as negative and is marked “0” in TABLE 12. When the 3 transitions of one and the same peptide are marked “1”, detection of the peptide is regarded as positive. One particular case is an exception to this rule. The peptide corresponding to the transitions numbered 49, 50 and 51 has a transition of very low intensity. In this precise case, when the transitions 49 and 50 are marked “1”, detection of this peptide will be regarded as positive.

TABLE 12 Transition number Smp21 Smp22 1 0 1 2 0 1 3 0 1 4 1 1 5 1 1 6 1 1 7 1 1 8 1 1 9 1 1 10 1 1 11 1 1 12 1 1 13 0 1 14 0 1 15 0 1 16 0 1 17 0 1 18 0 1 19 1 1 20 1 1 21 1 1 22 1 1 23 1 1 24 1 1 25 0 1 26 0 1 27 0 1 28 0 1 29 0 1 30 0 1 31 0 1 32 0 1 33 0 1 34 1 1 35 1 1 36 1 1 37 0 0 38 0 0 39 0 0 40 0 0 41 0 0 42 0 0 43 0 0 44 0 0 45 0 0 46 0 0 47 0 0 48 0 0 49 0 0 50 0 0 51 0 0 52 0 0 53 0 0 54 0 0 55 0 0 56 0 0 57 0 0 58 0 0 59 0 0 60 0 0 61 0 0 62 0 0 63 0 0 64 0 0 65 0 0 66 0 0 67 0 0 68 0 0 69 0 0 70 0 0 71 0 0 72 0 0 73 0 0 74 0 0 75 0 0 76 0 0 77 0 0 78 0 0 79 0 0 80 0 0 81 0 0 82 0 0 83 0 0 84 0 0 85 0 0 86 0 0 87 0 0 88 0 0 89 0 0 90 0 0 91 0 0 92 0 0 93 0 0 94 0 0 95 0 0 96 0 0 97 0 0 98 0 0 99 0 0 100 0 0 101 0 0 102 0 0 103 0 0 104 0 0 105 0 0 106 0 0 107 0 0 108 0 0 109 0 0 110 0 0 111 0 0 112 0 0 113 0 0 114 0 0 115 0 0 116 0 0 117 0 0 118 0 0 119 0 0 120 0 0 121 0 0 122 0 0 123 0 0 124 0 0 125 0 0 126 0 0 127 0 0 128 0 0 129 0 0 130 0 0 131 0 0 132 0 0 133 0 0 134 0 0 135 0 0 136 0 0 137 0 0 138 0 0 139 0 0 140 0 0 141 0 0 142 0 0 143 0 0 144 0 0 145 0 0 146 0 0 147 0 0 148 0 0 149 0 0 150 0 0 151 0 0 152 0 0 153 0 0

Samples Smp21 and Smp22 comprise at least one peptide characteristic of VanA. The bacteria present in samples Smp21 and Smp22 express the ligase VanA, which endows them with resistance to vancomycin and to teicoplanin.

Thus, particularly advantageously, a mechanism of inducible resistance, such as the mechanism of resistance linked to expression of VanA, is detected without an induction phase during culture of the microorganism, after a sample preparation phase performed in less than 3 hours. This method therefore allows quick investigation of the mechanisms of resistance to glycopeptides without a priori on their possible existence.

EXAMPLE 12 Identification of Resistance to Glycopeptides, without Induction

Samples Smp23 and Smp24 are identified according to one of the methods described in examples 1 to 6. Identification of the species is reported in TABLE 13.

TABLE 13 Name Species Smp23 E. faecium Smp24 E. faecalis Smp25 E. faecium

Samples Smp23, Smp24 and Smp25 correspond to the species Enterococcus faecalis or Enterococcus faecium, which may comprise a mechanism of resistance of the Van type.

The following method is then employed for investigating such a mechanism. Each sample is treated according to example 10, with the following modifications:

-   -   Step 1: a colony line of 3 cm is taken with a 10 μl loop         (against a colony previously).     -   Step 7: addition of 2 μg of trypsin.

Each sample is analyzed according to example 8 apart from the elements mentioned below.

The transitions mentioned in TABLE 3 are detected using the parameters shown in TABLES 4 and 11.

As in example 8, the positive areas are marked “1” in TABLE 14. The positive peptides are detected according to the rules of example 8.

TABLE 14 Transition number Smp23 Smp24 Smp25 1 0 0 1 2 0 0 1 3 0 0 1 4 0 0 1 5 0 0 1 6 0 0 1 7 0 0 1 8 0 0 1 9 0 0 1 10 0 0 1 11 0 0 1 12 0 0 1 13 0 0 0 14 0 0 0 15 0 0 0 16 0 0 0 17 0 0 0 18 0 0 0 19 0 0 1 20 0 0 1 21 0 0 1 22 0 0 1 23 0 0 1 24 0 0 1 25 0 0 1 26 0 0 1 27 0 0 1 28 0 0 1 29 0 0 1 30 0 0 1 31 0 0 1 32 0 0 1 33 0 0 1 34 0 0 1 35 0 0 1 36 0 0 1 37 1 0 0 38 1 0 0 39 1 0 0 40 1 0 0 41 1 0 0 42 1 0 0 43 1 0 0 44 1 0 0 45 1 0 0 46 1 0 0 47 1 0 0 48 1 0 0 49 1 0 0 50 1 0 0 51 1 0 0 52 1 0 0 53 1 0 0 54 1 0 0 55 1 0 0 56 1 0 0 57 1 0 0 58 0 0 0 59 0 0 0 60 0 0 0 61 0 0 0 62 0 0 0 63 0 0 0 64 0 0 0 65 0 0 0 66 0 0 0 67 0 0 0 68 0 0 0 69 0 0 0 70 0 0 0 71 0 0 0 72 0 0 0 73 0 0 0 74 0 0 0 75 0 0 0 76 0 0 0 77 0 0 0 78 0 0 0 79 0 0 0 80 0 0 0 81 0 0 0 82 0 0 0 83 0 0 0 84 0 0 0 85 0 0 0 86 0 0 0 87 0 0 0 88 0 0 0 89 0 0 0 90 0 0 0 91 1 0 1 92 1 0 1 93 0 0 0 94 0 0 0 95 0 0 0 96 0 0 0 97 0 0 0 98 0 0 0 99 0 0 0 100 0 0 0 101 0 0 0 102 0 0 0 103 0 0 0 104 0 0 0 105 0 0 0 106 0 0 0 107 0 0 0 108 0 0 0 109 0 0 0 110 0 0 0 111 0 0 0 112 0 0 0 113 0 0 0 114 0 0 0 115 0 0 0 116 0 0 0 117 0 0 0 118 0 0 0 119 0 0 0 120 0 0 0 121 0 0 0 122 0 0 0 123 0 0 0 124 0 0 0 125 0 0 0 126 0 0 0 127 0 0 0 128 0 0 0 129 0 0 0 130 0 0 0 131 0 0 0 132 0 0 0 133 0 0 0 134 0 0 0 135 0 0 0 136 0 0 0 137 0 0 0 138 0 0 0 139 0 0 0 140 0 0 0 141 0 0 0 142 0 0 0 143 0 0 0 144 0 0 0 145 0 0 0 146 0 0 0 147 0 0 0 148 0 0 0 149 0 0 0 150 0 0 0 151 0 0 0 152 0 0 0 153 0 0 0

Sample Smp23 comprises at least one peptide characteristic of VanB. The bacterium present in sample Smp23 expresses the ligase VanB, which endows it with resistance to vancomycin.

Sample Smp25 comprises at least one peptide characteristic of VanA. The bacterium present in sample Smp25 expresses the ligase VanA, which endows it with resistance to vancomycin and to teicoplanin.

Conversely, sample Smp24 does not have any peptide characteristic of resistance of the Van type. The bacterium present in sample Smp24 may be sensitive to the glycopeptides of the vancomycin or teicoplanin type.

Thus, particularly advantageously, a mechanism of inducible resistance, such as the mechanism of resistance linked to expression of VanB, is detected without an induction phase during culture of the microorganism, after a sample preparation phase performed in less than 3 hours. Also very advantageously, all the mechanisms of resistance to glycopeptides can be investigated and detected simultaneously. Thus, 2 mechanisms of resistance, VanB and VanA, are detected in samples Smp23 and Smp25 respectively using the same method. This method therefore allows quick investigation of the mechanisms of resistance to glycopeptides without a priori on their possible existence.

BIBLIOGRAPHIC REFERENCES

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The invention claimed is:
 1. A method of detection, for at least one microorganism contained in a sample, of at least one marker of resistance to a glycopeptide that is vancomycin, comprising detection, by MS/MS mass spectrometry in MRM mode, of at least one peptide of said microorganism selected from the Van type peptides of SEQ ID No. 5 to 16, 29 to 35, 59 to 71, 80 to 83, 85 to 91, 95 to 102, 104 to 120, 122 to 139 or 141 to
 154. 2. The method of detection as claimed in claim 1, comprising a step prior to the detection step of induction of a resistance mechanism by bringing said sample into contact with said glycopeptide beforehand.
 3. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanA type peptides of SEQ ID No. 5 to SEQ ID No.
 16. 4. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanA type peptides of SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 15, or SEQ ID No.
 16. 5. The method of detection as claimed in claim 2, in which said at least one peptide that is detected is selected from VanA type peptides of SEQ ID No. 5 to SEQ ID No.
 16. 6. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanB type peptides of SEQ ID No. 29 to SEQ ID No.
 35. 7. The method of detection as claimed in claim 2, in which said at least one peptide that is detected is selected from VanB type peptides of SEQ ID No. 29, SEQ ID No. 30, SEQ ID No. 32 or SEQ ID No.
 33. 8. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanC type peptides of SEQ ID No. 59 to SEQ ID No.
 71. 9. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanD type peptides of SEQ ID No. 80 to SEQ ID No.
 83. 10. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanD type peptides of SEQ ID No. 80, SEQ ID No. 81 or SEQ ID No.
 83. 11. The method of detection as claimed in claim 2, in which said at least one peptide that is detected is selected from VanD peptides of SEQ ID No. 80, SEQ ID No. 81 or SEQ ID No.
 83. 12. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanE type peptides of SEQ ID No. 85 to SEQ ID No.
 91. 13. The method of detection as claimed in claim 2, in which said at least one peptide that is detected includes VanE type peptide of SEQ ID No.
 89. 14. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanG type peptides of SEQ ID No. 95 to SEQ ID No.
 102. 15. The method of detection as claimed in claim 1, in which said at least one peptide that is detected includes at least one VanG type peptide of SEQ ID No. 97 or SEQ ID No.
 100. 16. The method of detection as claimed in claim 2, in which said at least one peptide that is detected is selected from VanG type peptides of SEQ ID No. 95, SEQ ID No. 96, SEQ ID No. 97, SEQ ID No. 98, SEQ ID No. 100 or SEQ ID No.
 102. 17. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanL type peptides of SEQ ID No. 104 to SEQ ID No.
 120. 18. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanM type peptides of SEQ ID No. 122 to SEQ ID No.
 139. 19. The method of detection as claimed in claim 1, in which said at least one peptide that is detected is selected from VanN type peptides of SEQ ID No. 141 to SEQ ID No.
 154. 20. A method of detecting at least one marker of resistance to a glycoprotein of at least one microorganism, comprising detecting whether at least one peptide that is any of SEQ ID NOs: 5-16, 29-35, 59-71, 80-83, 85-91, 95-102, 104-120, 122-139, or 141-154 is present in a sample by mass spectrometry.
 21. The method as claimed in claim 20, wherein the mass spectrometry is MS/MS mass spectrometry.
 22. The method as claimed in claim 20, further comprising contacting the sample with the glycoprotein before detection.
 23. The method as claimed in claim 22, wherein the glycoprotein is vancomycin. 